NOVEL SURFACE EXPOSED HAEMOPHILUS INFLUENZA PROTEIN (PROTEIN E; pE)

ABSTRACT

The present invention relates to a surface exposed protein (protein E; pE), a virulence factor, which can be detected in  Haemophilus influenzae,  having an amino acid sequence as described in SEQ ID NO 1, an immunogenic fragment of said surface exposed protein, and a recombinant immunogenic protein (pE(A)) or truncated variants thereof based on said surface exposed protein. Nucleic acid sequences, vaccines, plasmids and phages, non human hosts, recombinant nucleic acid sequences, fusion proteins and fusion products are also described. A method of producing the said protein or truncated fragments thereof recombinantly is also disclosed.

This application is a divisional of U.S. patent application Ser. No.14/085,007, filed on Nov. 20, 2013, which is a divisional of U.S. patentapplication Ser. No. 12/161,040, now U.S. Pat. No. 8,617,565, issuedDec. 31, 2013, which has a §371 date of Nov. 18, 2008, and which is theU.S. national stage application of International Application No.PCT/SE2007/00034, filed on Jan. 17, 2007, which claims the benefit ofpriority of U.S. Provisional Application No. 60/758,987, filed on Jan.17, 2006. All of these applications are herein incorporated by referencein their entireties.

FIELD OF THE INVENTION

The present invention relates to the surface exposed protein E, avirulence factor, which exists in all encapsulated and non-typableHaemophilus influenzae.

BACKGROUND OF THE INVENTION

Both Haemophilus influenzae type b (Hib) and non-typeable H. influenzae(NTHi) cause a variety of diseases in children and in adults. Hib causesbacterial meningitis and other invasive infections in children under theage of 4 years, whereas NTHi has been isolated from cases of otitismedia, sinusitis, epiglottitis, tracheobronchitis, and pneumonia and maycause neonatal sepsis. There is currently no commercially availablevaccine against NTHi, but a number of vaccines are in use against Hib.These vaccines consist of the Hib capsular polysaccharide, polyribosylribitol phosphate, conjugated to various protein carriers (meningococcolouter membrane complex, tetanus toxoid, nontoxic mutant diphtheriatoxin, or diphtheria toxoid) to overcome the weak immune response tocapsular polysaccharide in children younger than 18 months of age. H.influenzae outer membrane proteins (OMPs) are also considered to becarriers of polyribosyl ribitol phosphate since they are shown to betargets of host antibodies following Hib and NTHi infections. Antibodiesto OMPs P1, P2, P4, P5, and P6 and a 98-kDa protein have been tested inin vivo protection and in vitro bactericidal assays against H.influenzae infections, with antibodies to P1, P4, and P6 showingbiological activity against both homologous and heterologous H.influenzae strains. The lack of heterologous protection from antibodiesto other OMPs is partly due to the antigenic diversity of these proteinsamong different H. influenzae strains. An ideal antigen must thereforebe both exposed on the bacterial surface and antigenically wellconserved. In this laboratory, a 42-kDa membrane protein (protein D)that is widely distributed and antigenically conserved among both Hiband NTHi strains has been isolated, cloned, sequenced, and shown to be apathogenicity factor and a possible vaccine candidate (1-5).

Two decades ago, Haemophilus influenzae and M. catarrhalis were shown todisplay a strong affinity for both soluble and surface-bound human IgD(6). The IgD-binding seems to be paralleled by a similar interactionwith surface-bound IgD at the cellular level, a phenomenon that explainsthe strong mitogenic effects on human lymphocytes by H. influenzae andM. catarrhalis (7-9). An IgD-binding outer membrane protein from H.influenzae (protein D) was isolated and cloned, and shown to be animportant pathogenicity factor (1-5). However, protein D does not binduniversally to all IgD myelomas(10).

SUMMARY OF THE INVENTION

In view of the fact that H. influenzae has been found to be such aleading cause of infections in the upper and lower airways, there is acurrent need to develop vaccines that can be used against H. influenzae.

The aim of the present invention has therefore been to find out in whichway H. influenzae interacts with cells in the body and interacts withthe immune system, and be able to provide a new type of vaccine.

According to one aspect, the present invention provides a surfaceexposed protein, which can be detected in Haemophilus influenzae, havingan amino acid sequence according to SEQ ID NO: 1, or a fragment,homologue, functional equivalent, derivative, degenerate orhydroxylation, sulphonation or glycosylation product or other secondaryprocessing product thereof.

According to another aspect the present invention provides animmunogenic fragment of said surface exposed protein, which fragment canbe detected in Haemophilus influenzae, or naturally occurring orartificially modified variants thereof.

According to a further aspect the present invention provides arecombinant immunogenic protein based on the surface exposed proteinmentioned above, wherein the amino acids in position 1 to 21 of SEQ IDNO: 1 have been deleted or replaced by one or more amino acids. In oneembodiment the amino acids in position 1 to 21 of SEQ ID NO: 1 have beenreplaced by a sequence of 0 to 21 optional amino acids. In anotherembodiment the recombinant immunogenic protein have an amino acidsequence according to SEQ ID NO: 2, or a fragment, homologue, functionalequivalent, derivative, degenerate or hydroxylation, sulphonation orglycosylation product or other secondary processing product thereof.

According to a further aspect the present invention provides a peptidehaving an amino acid sequence according to SEQ ID NO: 3, or a fragment,homologue, functional equivalent, derivative, degenerate orhydroxylation, sulphonation or glycosylation product or other secondaryprocessing product thereof.

According to still a further aspect the present invention provides apeptide having an amino acid sequence according to SEQ ID NO: 4, or afragment, homologue, functional equivalent, derivative, degenerate orhydroxylation, sulphonation or glycosylation product or other secondaryprocessing product thereof.

According to yet a further aspect the present invention provides apeptide having an amino acid sequence according to SEQ ID NO: 5, or afragment, homologue, functional equivalent, derivative, degenerate orhydroxylation, sulphonation or glycosylation product or other secondaryprocessing product thereof.

According to a further aspect the present invention provides a peptidehaving an amino acid sequence according to SEQ ID NO: 6, or a fragment,homologue, functional equivalent, derivative, degenerate orhydroxylation, sulphonation or glycosylation product or other secondaryprocessing product thereof.

According to still a further aspect the present invention provides apeptide having an amino acid sequence according to SEQ ID NO: 7, or afragment, homologue, functional equivalent, derivative, degenerate orhydroxylation, sulphonation or glycosylation product or other secondaryprocessing product thereof.

According to yet a further aspect the present invention provides apeptide having an amino acid sequence according to SEQ ID NO: 8, or afragment, homologue, functional equivalent, derivative, degenerate orhydroxylation, sulphonation or glycosylation product or other secondaryprocessing product thereof.

According to a further aspect the present invention provides a peptidehaving an amino acid sequence according to SEQ ID NO: 9, or a fragment,homologue, functional equivalent, derivative, degenerate orhydroxylation, sulphonation or glycosylation product or other secondaryprocessing product thereof.

According to another aspect the present invention provides a peptidehaving an amino acid sequence according to SEQ ID NO: 10, or a fragment,homologue, functional equivalent, derivative, degenerate orhydroxylation, sulphonation or glycosylation product or other secondaryprocessing product thereof.

According to another aspect the present invention provides the use of atleast one protein, fragment or peptide as described above for themanufacturing of a medicament for the prophylaxis or treatment of aninfection. In one embodiment the infection is caused by Haemophilusinfluenzae, and in another embodiment the Haemophilus influenzae isencapsulated or non-typable. In still another embodiment, said use isfor the prophylaxis or treatment of otitis media, sinusitis or lowerrespiratory tract infections, in children as well as adults with, forexample, chronic obstructive pulmonary disease (COPD).

According to one aspect, the present invention provides a medicamentcomprising at least one protein, fragment or peptide as described aboveand one or more pharmaceutically acceptable adjuvants, vehicles,excipients, binders, carriers, preservatives, buffering agents,emulsifying agents, wetting agents, or transfection facilitatingcompounds.

According to another aspect, the present invention provides a vaccinecomposition comprising at least one protein, fragment or peptide asdescribed above. In one embodiment, said vaccine composition comprisesat least one di-, tri- or multimer of said protein, fragment or peptide.In another embodiment, the vaccine composition, further comprises one ormore pharmaceutically acceptable adjuvants, vehicles, excipients,binders, carriers, preservatives, buffering agents, emulsifying agents,wetting agents, or transfection facilitating compounds. In still anotherembodiment, said vaccine composition comprises at least one furthervaccine, and in yet another embodiment it comprises an immunogenicportion of another molecule, wherein the immunogenic portion of anothermolecule can be chosen from the group comprising Protein D of H.influenzae (EP 594 610), MID of Moraxella catarrhalis (WO 03/004651, WO97/41731 and WO96/34960), UspA1 or UspA2 of Moraxella catarrhalis(WO93/03761), and outer membrane protein or carbohydrate capsule, of anyrespiratory tract pathogen, or DNA oligonucleotides, such as CpG motif.In one aspect the present invention relates to a nucleic acid sequenceencoding a protein, fragment or peptide as described above, as well ashomologues, polymorphisms, degenerates and splice variants thereof. Inone embodiment, said nucleic acid sequence is fused to at least anothergene.

In another aspect the present invention relates to a plasmid or phagecomprising a nucleic acid sequence as described above.

In yet another embodiment the present invention relates to a non humanhost comprising at least one plasmid as described above and capable ofproducing a protein, fragment or peptide as discussed above, as well ashomologues, polymorphisms, degenerates and splice variants thereof,which host is chosen among bacteria, yeast and plants. In oneembodiment, said host is E. coli.

In still another aspect, the present invention provides a fusion proteinor polypeptide, in which a protein, fragment or peptide as describedabove is combined with at least another protein by the use of arecombinant nucleic acid sequence as discussed above. In one embodiment,said fusion protein is a di-, tri or multimer of a protein, fragment orpeptide as discussed above.

In one aspect, the present invention relates to a fusion product, inwhich a protein, fragment or peptide as described above is covalently,or by any other means, bound to a protein, carbohydrate or matrix.

In yet another aspect the present invention relates to a method ofisolation of a protein, fragment or peptide as described above, saidmethod comprising the steps:

a) growing Haemophilus influenzae or E. coli comprising the DNA codingfor said protein, fragment or peptide, harvesting the bacteria andisolating outer membranes or inclusion bodies;

b) solubilizing the inclusion bodies with a strong solvatising agent;

c) adding a renaturating agent; and

d) dialyzing the resulting suspension against a buffer with a pH of from8 to 10.

In one embodiment of said method the solvalising agent is guanidiumhydrochloride, and in another embodiment the renaturating agent isarginin.

In another aspect the present invention relates to a medicament or avaccine composition as discussed above, comprising said fusion proteinor polypeptide, or said fusion product.

In one aspect the present invention relates to a method of preventing ortreating an infection in an individual comprising administering apharmaceutically effective amount of a medicament or a vaccinecomposition as described above. In one embodiment said infection iscaused by Haemophilus influenzae, both encapsulated or non-typable, andin yet another embodiment the infection is chosen from the groupconsisting of otitis media, sinusitis or lower respiratory tractinfections.

The present invention relates to Protein E, in particular Protein Epolypeptides and Protein E polynucleotides, recombinant materials andmethods for their production. In another aspect, the invention relatesto methods for using such polypeptides and polynucleotides, includingprevention and treatment of microbial diseases, amongst others. In afurther aspect, the invention relates to diagnostic assays for detectingdiseases associated with microbial infections and conditions associatedwith such infections, such as assays for detecting expression oractivity of Protein E polynucleotides or polypeptides.

Various changes and modifications within the spirit and scope of thedisclosed invention will become readily apparent to those skilled in theart from reading the following descriptions and from reading the otherparts of the present disclosure.

DESCRIPTION OF THE FIGURES

FIG. 1. The 16.3 kDa Haemophilus influenzae protein E is detected by anIgD(λ) myeloma protein. In A, flow cytometry analysis of pE expressionin H. influenzae 772 is demonstrated. SDS-PAGE and Western blot (B) and2-dimensional SDS-polyacrylamide gel electrophoresis analyses (C) ofEmpigen®-treated outer membrane proteins of H. influenzae MinnA isshown. Outer membrane protein extracts are shown before (B) and afterseparation on Q-Sepharose (C). The arrow in panel C indicates thepredicted localization for pE based upon a Western blot (using IgD(λ) asa probe) of a corresponding gel. In A, bacteria were loaded with IgD(λ)myeloma protein followed by incubation with rabbit FITC-conjugatedanti-IgD pAb and flow cytometry analysis. In B, a Coomassie blue stainedSDS-gel (stain) and Western blot probed with human myeloma IgD(λ)followed by incubation with horseradish peroxidase-conjugated goatanti-human IgD polyclonal antibodies are shown. Samples were boiled inthe presence of 2-mercaptoethanol for 10 min prior to loading.

FIG. 2. Flow cytometry profiles of pE-expressing E. coli compared to theH. influenzae 3655 wild type and a pE deficient mutant. E. coliharbouring an empty pUC18 vector (A) is compared to bacteria transformedwith pUC18 containing genomic DNA from H. influenzae 772 (genes HI0175to HI0178) (B). pE expression in the non-typable H. influenzae 3655 wildtype (C) and the corresponding mutant (D) is shown. E. coli strain JM83and H. influenzae were grown in liquid cultures overnight. E. coli wasincubated with human myeloma IgD(λ) on ice. After 1 h and washings,FITC-conjugated rabbit anti-human IgD pAb was added for an additional 30min followed by washing steps and subsequent flow cytometry analysis.The same procedure was done with H. influenzae 3655 or the derived pEmutant using specific rabbit anti-pE polyclonal antibodies andFITC-conjugated goat anti-rabbit pAb.

FIG. 3. pE expression of H. influenzae and related species as revealedby flow cytometry and an IgD(λ) myeloma serum. Twenty-two strains ofNTHi and 27 strains of haemophilus species or related bacteria wereanalysed. Bacteria were grown to stationary phase and incubated with ahuman myeloma IgD(λ) on ice. After 1 h and washings, FITC-conjugatedrabbit anti-human IgD polyclonal antibodies (pAb) were added for anadditional 30 min followed by washing steps and subsequent flowcytometry analyses.

FIG. 4. pE is expressed in NTHi and encapsulated H. influenzae asrevealed by Western blots. Bacterial proteins from the indicated strainswere prepared using Empigen® and subjected to a SDS-gel followed byWestern blot probed with human myeloma IgD(λ) and horseradishperoxidase-conjugated goat anti-human IgD polyclonal pAb as detectionantibodies.

FIG. 5. Recombinant pE22-160 based upon the sequence from NTHi 772 ascompared to native pE from H. influenzae MinnA. In A, the amino-terminalsequence of the pE-derived fragment A (SEQ ID NO: 32) compared with thepredicted amino-terminal sequence of native protein pE (SEQ ID NO: 31).In B, a schematic illustration of pE(A) with the Histidine tag (SEQ IDNO: 12) is shown (MDIGINSDP disclosed as SEQ ID NO: 33). In C, the sizeand purity is demonstrated on a Commassie-stained PAGE. In D and E, anouter membrane protein (OMP) extract from H. influenzae MinnA iscompared to recombinantly produced pE(A) in a Coomassie-stained gel andWestern Blot, respectively. In A, the signal peptide sequence wasremoved in addition to the amino acid residue glutamine 21. Nine aminoacids were derived from the expression vector pET26(+) as indicated.Numbers represent amino acid positions beginning from the translationalstart of pE. Recombinant pE(A) was produced in E. coli, purified, andsubjected to Edman degradation in order to analyse the signal peptidasecleavage site. In D and E, two gels were run simultaneously, one wasstained with Coomassie brilliant blue and one was blotted ontoImmobilon-P membranes, probed with human IgD(λ) myeloma protein followedby incubation with appropriate horseradish peroxidase-conjugatedsecondary antibodies. The OMP fraction was purified using Empigen® asdescribed in Material and Methods.

FIG. 6. Protein E is extraordinary conserved. The frequency of pointmutations in 13 to 31 Haemophilus influenzae strains (Table 2) includingboth encapsulated and non-typable isolates are shown. Results wereobtained by sequencing using flanking primers. All sequences werecompared to the pE sequence of H. influenzae Rd that was used as areference sequence and is shown here (the DNA sequence is SEQ ID NO: 34and the protein sequence is SEQ ID NO: 35).

FIG. 7. The hydropathy profile of pE. The hydrophobic and hydrophilicparts of the individual amino acid residues are indicated. The predictedsignal peptide is also outlined. Data was obtained by using a standardmethod as described (21).

FIG. 8. SDS-PAGE demonstrating recombinant pE22-160 (fragment A) and aseries of truncated fragments designated B to H. In A, an outline of thedifferent fragments are shown, whereas in B, an SDS-PAGE isdemonstrated. DNA encoding the various proteins were ligated into theexpression vector pET26(+) and recombinantly expressed in E. coli.Resulting overexpressed proteins were purified on nickel resins andsubjected to separation on a SDS-PAGE followed by Coomassie brilliantblue staining.

FIG. 9. A pE-deficient mutant strain (NTHi 3655) has a 100 to 1,000-foldlower capacity to induce acute otitis media in rats. Infection wasinduced in male Sprague-Dawley rats by a ventral midline incision in theneck followed by injection into the middle ear cavity of the indicatednumbers of bacteria in 0.05 ml. The data shown is from day 3 ofchallenge and is representative of five animals in each group.

FIG. 10. Mean concentrations of IgG and IgA antibodies directed againstpE in sera from different age groups. Anti-pE antibodies were analysedby a sandwich ELISA using recombinant pE(A) as bate. The purity of pE(A)was as indicated in FIG. 5.

FIG. 11. pE is extraordinary conserved within different haemophilusstrains. The pe gene was sequenced in encapsulated H. influenzae type a(n=2), b (n=2), c (n=2), d (n=1), e (n=2), and f (n=3), NTHi (n=8), H.influenzae biovar aegypticus (n=6) and H. aegypticus (n=5), usingflanking primers. Rd designates H. influenzae strain Rd (Hi0178) and 772the NTHi strain 772. The numbers 65 to 577 correspond to the strainsoutlined in Table 1. The 32 listed sequences correlate to SEQ ID NO: 36,1, 37, 38, 39, 40, 41, 42, 43, 44, 45, 45, 46, 47, 46, 48, 49, 50, 42,51, 52, 53, 54, 55, 56, 57, 58, 59, 36, 60, 61, 62, respectively, inorder of appearance from top to bottom).

DESCRIPTION OF THE INVENTION

Before explaining the present invention in detail, it is important tounderstand that the invention is not limited in this application to thedetails of the embodiments and steps described herein. The examplesmentioned are illustrative of the invention but do not limit it in anyway. The invention is capable of other embodiments and of beingpracticed or carried out in a variety of ways. It is to be understoodthat the phraseology and terminology employed herein is for the purposeof description and not of limitation.

The present application describes the cloning and expression of a novelH. influenzae outer membrane protein designated protein E (pE). Theprotein was discovered using a human IgD (λ) myeloma serum with specificaffinity for pE.

To maximize the yield of recombinant pE, a truncated pE fragmentconsisting of amino acid residues lysine22 to lysine160 wasmanufactured. The N-terminal signal peptide including the amino acidglutamine2l was thus removed and replaced with the leader peptide inaddition to nine residues originating from the vector pET26(+). Thetruncated pE (i.e., pE22-160) was designated pE(A).

The present invention comprises the Haemophilus outer membrane proteinpE and the pE-derived peptides pE22-60, pE22-95, pE22-125, pE41-68,pE56-125, pE56-160, pE86-160, pE115-160, and di-, tri- or oligomersthereof. In particular, sequences of pE or the derived peptides that aresurface exposed are given a higher priority

Thus, the vaccine compositions according to the present inventioncomprises as immunogenic components a surface exposed protein, which canbe detected in all Haemophilus influenzae, an immunogenic fragment ofsaid surface exposed protein, a recombinant immunogenic protein based onsaid surface exposed protein, a recombinant immunogenic protein havingan amino acid sequence according to SEQ ID NO: 2, and/or a peptidehaving an amino acid sequence according to SEQ ID NO: 3-10, or afragment, homologue, functional equivalent, derivative, degenerate orhydroxylation, sulphonation or glycosylation product or other secondaryprocessing product thereof. The vaccine compositions may also comprise afusion protein or polypeptide, or a fusion product according to thepresent invention as immunogenic components. The immunogenic componentsare capable of eliciting an antibody or other immune response toHaemophilus influenzae, wherein the antibodies elicited inhibit thepathogenesis of Haemophilus influenzae bacterium to the cells of thesubject. An “immunogenic dose” of a vaccine composition according to theinvention is one that generates, after administration, a detectablehumoral and/or cellular immune response in comparison to a standardimmune response before administration.

The nucleic sequences used in the vaccine compositions of the presentinvention to generate the antigens may be inserted into any of a widevariety of expression vectors by a variety of procedures. Suchprocedures are deemed to be known by those skilled in the art.

Vaccine compositions are easily accomplished using well known methodsand techniques, and can be administered in a variety of ways, preferablyparenterally or intranasally. Formulations suitable for parenteral orintranasal administration include aqueous and non-aqueous sterileinjection solutions which may contain antioxidants, buffers,bacteriostats and solutes that makes the formulation isotonic with thebodily fluid of the subject in question; and aqueous and non-aqueoussterile suspensions which may include suspending agents or thickeningagents. The active immunogenic ingredient is often mixed with excipientswhich are pharmaceutically acceptable, e g water, saline, dextrose,glycerol, ethanol, or the like. In addition, the vaccine composition canalso contain minor amounts of auxiliary substances such as wetting oremulsifying agents, pH buffering agents, binders, carriers orpreservatives.

The vaccine compositions may also include adjuvants for enhancing theimmunogenicity of the composition, such as Freund's Adjuvants and othersystems known in the art. The immunogenic components of the vaccinecompositions, ie the proteins, fragments, peptides, fusion proteins orpolypeptides, or fusion products of the present invention, may beformulated into the vaccine as neutral or salt forms.

The dosage of the vaccine compositions will depend on the specificactivity of the vaccine and can be readily determined by routineexperimentation. The vaccine compositions are administered in such anamount as will be therapeutically effective and immunogenic, and thequantity depends on the subject.

The invention relates to Protein E polypeptides and polynucleotides asdescribed in greater detail below. In particular, the invention relatesto polypeptides and polynucleotides of Protein E of non typeable H.Influenzae. The Protein E polypeptides have a signal sequence and areexposed at the surface of the bacteria. The signal peptide is locatedfrom residue 1 to residue 20 of Protein E polypeptide.

A reference to “Protein E” herein is a reference to any of the peptides,immunogenic fragments, fusions, polypeptides or proteins of theinvention discussed herein (such as SEQ ID NO:1 with or without thesignal sequence). A “polynucleotide encoding Protein D” refers to anypolynucleotide sequence encoding any of the peptides, immunogenicfragments, fusions, polypeptides or proteins of the invention discussedherein.

The term “comprising” herein alternatively may be substituted with theterm “consisting of”.

The invention relates especially to Protein E polynucleotides andencoded polypeptides listed herein.

It is understood that sequences recited in the Sequence Listing below as“DNA” represent an exemplification of one embodiment of the invention,since those of ordinary skill will recognize that such sequences can beusefully employed in polynucleotides in general, includingribopolynucleotides.

The sequences of the Protein E polynucleotides are set out in SEQ IDNO:-11 (from ntHi strain 772). The sequences of the Protein E encodedpolypeptides are set out in SEQ ID NO:1 (from ntHi strain 772), 2, 3, 4,5, 6, 7, 8, 9, 10.

Polypeptides

In one aspect of the invention there are provided polypeptides of H.influenzae (in particular non typeable H. influenzae) referred to hereinas “Protein E” and “Protein E polypeptides” as well as biologically,diagnostically, prophylactically, clinically or therapeutically usefulvariants thereof, and compositions comprising the same.

The present invention further provides for:

(a) an isolated polypeptide which comprises an amino acid sequence whichhas at least 85% identity, preferably at least 90% identity, morepreferably at least 95% identity, most preferably at least 97-99% orexact identity, to that of any sequence of SEQ ID NO: 1-10;

(b) a polypeptide encoded by an isolated polynucleotide comprising apolynucleotide sequence which has at least 85% identity, preferably atleast 90% identity, more preferably at least 95% identity, even morepreferably at least 97-99% or exact identity to any sequence of SEQ IDNO: 11 over the entire length of the selected sequence of SEQ ID NO: 11;or

(c) a polypeptide encoded by an isolated polynucleotide comprising apolynucleotide sequence encoding a polypeptide which has at least 85%identity, preferably at least 90% identity, more preferably at least 95%identity, even more preferably at least 97-99% or exact identity, to theamino acid sequence of any sequence of SEQ ID NO: 1-10.

The Protein E polypeptides provided in SEQ ID NO: 1-10 are the Protein Epolypeptides from non typeable H. influenzae strains. Further Protein Esequences have been ascertained from H. influenzae strains listed inTable 1.

The invention also provides an immunogenic fragment of a Protein Epolypeptide, that is, a contiguous portion of the Protein E polypeptidewhich has the same or substantially the same immunogenic activity as thepolypeptide comprising the corresponding amino acid sequence selectedfrom SEQ ID NO: 1-10; That is to say, the fragment (if necessary whencoupled to a carrier) is capable of raising an immune response whichrecognises the Protein E polypeptide. Alternatively, or in addition, theimmunogenic fragment may retain an IgD binding function of the fulllength protein (as described in the Example section, for instance thecapability to bind IgD(λ) from The Binding Site (Birmingham, England).Such an immunogenic fragment may include, for example, the Protein Epolypeptide lacking an N-terminal leader sequence, and/or atransmembrane domain and/or a C-terminal anchor domain. In a preferredaspect the immunogenic fragment of Protein E according to the inventioncomprises substantially all of the extracellular domain of a polypeptidewhich has at least 85% identity, preferably at least 90% identity, morepreferably at least 95% identity, most preferably at least 97-99%identity, to that a sequence selected from SEQ ID NO: 1-10 over theentire length of said sequence.

A fragment is a polypeptide having an amino acid sequence that isentirely the same as part but not all of any amino acid sequence of anypolypeptide of the invention. As with Protein E polypeptides, fragmentsmay be “free-standing,” or comprised within a larger polypeptide ofwhich they form a part or region, most preferably as a single continuousregion in a single larger polypeptide. A fragment may therefore beshorter than the full-length native sequence, or, if comprised within alarger polypeptide, may be a full length native sequence or a longerfusion protein.

Preferred fragments include, for example, truncation polypeptides havinga portion of an amino acid sequence selected from SEQ ID NO: 1-10 or ofvariants thereof, such as a continuous series of residues that includesan amino- and/or carboxyl-terminal amino acid sequence. Degradationforms of the polypeptides of the invention produced by or in a hostcell, are also preferred. Further preferred are fragments characterizedby structural or functional attributes such as fragments that comprisealpha-helix and alpha-helix forming regions, beta-sheet andbeta-sheet-forming regions, turn and turn-forming regions, coil andcoil-forming regions, hydrophilic regions, hydrophobic regions, alphaamphipathic regions, beta amphipathic regions, flexible regions,surface-forming regions, substrate binding region, and high antigenicindex regions.

Further preferred fragments include an isolated polypeptide comprisingan amino acid sequence having at least 15, 20, 30, 40, 50 or 100contiguous amino acids from an amino acid sequence selected from SEQ IDNO: 1-10 or an isolated polypeptide comprising an amino acid sequencehaving at least 15, 20, 30, 40, 50 or 100 contiguous amino acidstruncated or deleted from an amino acid sequence selected from SEQ IDNO: 1-10.

Still further preferred fragments are those which comprise a B-cellepitope, for example those fragments/peptides described in Example 10.

Fragments of the polypeptides of the invention may be employed forproducing the corresponding full-length polypeptide by peptidesynthesis; therefore, these fragments may be employed as intermediatesfor producing the full-length polypeptides of the invention.

Particularly preferred are variants in which several, 5-10, 1-5, 1-3,1-2 or 1 amino acids are substituted, deleted, or added in anycombination.

The polypeptides, or immunogenic fragments, of the invention may be inthe form of the “mature” protein or may be a part of a larger proteinsuch as a precursor or a fusion protein. It is often advantageous toinclude an additional amino acid sequence which contains secretory orleader sequences, pro-sequences, sequences which aid in purificationsuch as multiple histidine residues, or an additional sequence forstability during recombinant production. Furthermore, addition ofexogenous polypeptide or lipid tail or polynucleotide sequences toincrease the immunogenic potential of the final molecule is alsoconsidered.

In one aspect, the invention relates to genetically engineered solublefusion proteins comprising a polypeptide of the present invention, or afragment thereof, and various portions of the constant regions of heavyor light chains of immunoglobulins of various subclasses (IgG, IgM, IgA,IgE). Preferred as an immunoglobulin is the constant part of the heavychain of human IgG, particularly IgG1, where fusion takes place at thehinge region. In a particular embodiment, the Fc part can be removedsimply by incorporation of a cleavage sequence which can be cleaved withblood clotting factor Xa.

Furthermore, this invention relates to processes for the preparation ofthese fusion proteins by genetic engineering, and to the use thereof fordrug screening, diagnosis and therapy. A further aspect of the inventionalso relates to polynucleotides encoding such fusion proteins. Examplesof fusion protein technology can be found in International PatentApplication Nos. WO94/29458 and WO94/22914.

The proteins may be chemically conjugated, or expressed as recombinantfusion proteins allowing increased levels to be produced in anexpression system as compared to non-fused protein. The fusion partnermay assist in providing T helper epitopes (immunological fusionpartner), preferably T helper epitopes recognised by humans, or assistin expressing the protein (expression enhancer) at higher yields thanthe native recombinant protein. Preferably the fusion partner will beboth an immunological fusion partner and expression enhancing partner.

Fusion partners include protein D from Haemophilus influenzae (EP594610) and the non-structural protein from influenza virus, NS1(hemagglutinin). Another fusion partner is the protein known as Omp26(WO 97/01638). Another fusion partner is the protein known as LytA.Preferably the C terminal portion of the molecule is used. LytA isderived from Streptococcus pneumoniae which synthesize anN-acetyl-L-alanine amidase, amidase LytA, (coded by the lytA gene {Gene,43 (1986) page 265-272}) an autolysin that specifically degrades certainbonds in the peptidoglycan backbone. The C-terminal domain of the LytAprotein is responsible for the affinity to the choline or to somecholine analogues such as DEAE. This property has been exploited for thedevelopment of E. coli C-LytA expressing plasmids useful for expressionof fusion proteins. Purification of hybrid proteins containing theC-LytA fragment at its amino terminus has been described {Biotechnology:10, (1992) page 795-798}. It is possible to use the repeat portion ofthe LytA molecule found in the C terminal end starting at residue 178,for example residues 188-305.

The present invention also includes variants of the aforementionedpolypeptides, that is polypeptides that vary from the referents byconservative amino acid substitutions, whereby a residue is substitutedby another with like characteristics. Typical such substitutions areamong Ala, Val, Leu and Ile; among Ser and Thr; among the acidicresidues Asp and Glu; among Asn and Gln; and among the basic residuesLys and Arg; or aromatic residues Phe and Tyr.

Polypeptides of the present invention can be prepared in any suitablemanner. Such polypeptides include isolated naturally occurringpolypeptides, recombinantly produced polypeptides, syntheticallyproduced polypeptides, or polypeptides produced by a combination ofthese methods. Means for preparing such polypeptides are well understoodin the art.

It is most preferred that a polypeptide of the invention is derived fromnon typeable H. influenzae, however, it may preferably be obtained fromother organisms of the same taxonomic genus. A polypeptide of theinvention may also be obtained, for example, from organisms of the sametaxonomic family or order.

Polynucleotides

It is an object of the invention to provide polynucleotides that encodeProtein E polypeptides, particularly polynucleotides that encode thepolypeptides herein designated Protein E.

In a particularly preferred embodiment of the invention thepolynucleotides comprise a region encoding Protein E polypeptidescomprising sequences set out in SEQ ID NO: 11 which include full lengthgene, or a variant thereof.

The Protein E polynucleotides provided in SEQ ID NO: 11 are the ProteinE polynucleotides from non typeable H. influenzae strain 772. Othersequences have been determined of genes encoding protein E from H.influenzae strains listed in Table 1.

As a further aspect of the invention there are provided isolated nucleicacid molecules encoding and/or expressing Protein E polypeptides andpolynucleotides, particularly non typeable H. influenzae Protein Epolypeptides and polynucleotides, including, for example, unprocessedRNAs, ribozyme RNAs, mRNAs, cDNAs, genomic DNAs, B- and Z-DNAs. Furtherembodiments of the invention include biologically, diagnostically,prophylactically, clinically or therapeutically useful polynucleotidesand polypeptides, and variants thereof, and compositions comprising thesame.

Another aspect of the invention relates to isolated polynucleotides,including at least one full length gene, that encodes a Protein Epolypeptide having a deduced amino acid sequence of SEQ ID NO: 1-10 andpolynucleotides closely related thereto and variants thereof.

In another particularly preferred embodiment of the invention relates toProtein E polypeptide from non typeable H. influenzae comprising orconsisting of an amino acid sequence selected from SEQ ID NO: 1-10 or avariant thereof.

Using the information provided herein, such as a polynucleotidesequences set out in SEQ ID NO: 11, a polynucleotide of the inventionencoding Protein E polypeptides may be obtained using standard cloningand screening methods, such as those for cloning and sequencingchromosomal DNA fragments from bacteria using non typeable H. influenzaestrain3224A (or 772) cells as starting material, followed by obtaining afull length clone. For example, to obtain a polynucleotide sequence ofthe invention, such as a polynucleotide sequence given in SEQ ID NO: 11,typically a library of clones of chromosomal DNA of non typeable H.influenzae strain 3224A (or 772) in E. coli or some other suitable hostis probed with a radiolabeled oligonucleotide, preferably a 17-mer orlonger, derived from a partial sequence. Clones carrying DNA identicalto that of the probe can then be distinguished using stringenthybridization conditions. By sequencing the individual clones thusidentified by hybridization with sequencing primers designed from theoriginal polypeptide or polynucleotide sequence it is then possible toextend the polynucleotide sequence in both directions to determine afull length gene sequence. Conveniently, such sequencing is performed,for example, using denatured double stranded DNA prepared from a plasmidclone. Suitable techniques are described by Maniatis, T., Fritsch, E. F.and Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL, 2nd Ed.;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989).(see in particular Screening By Hybridization 1.90 and SequencingDenatured Double-Stranded DNA Templates 13.70). Direct genomic DNAsequencing may also be performed to obtain a full length gene sequence.Illustrative of the invention, the polynucleotide set out in SEQ ID NO:11 was discovered in a DNA library derived from non typeable H.influenzae.

Moreover, each DNA sequence set out in SEQ ID NO: 11 contains an openreading frame encoding a protein having about the number of amino acidresidues set forth in SEQ ID NO:-1 with a deduced molecular weight thatcan be calculated using amino acid residue molecular weight values wellknown to those skilled in the art.

The polynucleotides of SEQ ID NO: 11, between the start codon and thestop codon, encode respectively the polypeptide of SEQ ID NO: 1.

In a further aspect, the present invention provides for an isolatedpolynucleotide comprising or consisting of:

-   (a) a polynucleotide sequence which has at least 85% identity,    preferably at least 90% identity, more preferably at least 95%    identity, even more preferably at least 97-99% or exact identity, to    any polynucleotide sequence from SEQ ID NO: 11 over the entire    length of the polynucleotide sequence from SEQ ID NO: 11; or-   (b) a polynucleotide sequence encoding a polypeptide which has at    least 85% identity, preferably at least 90% identity, more    preferably at least 95% identity, even more preferably at least    97-99% or 100% exact identity, to any amino acid sequence selected    from SEQ ID NO: 1-10 (or fragment thereof), over the entire length    of the amino acid sequence from SEQ ID NO: 1-10 (or fragment).

A polynucleotide encoding a polypeptide of the present invention,including homologs and orthologs from species other than non typeable H.influenzae, may be obtained by a process which comprises the steps ofscreening an appropriate library under stringent hybridizationconditions (for example, using a temperature in the range of 45-65° C.and an SDS concentration from 0.1-1%) with a labeled or detectable probeconsisting of or comprising any sequence selected from SEQ ID NO: 11 ora fragment thereof; and isolating a full-length gene and/or genomicclones containing said polynucleotide sequence.

The invention provides a polynucleotide sequence identical over itsentire length to a coding sequence (open reading frame) set out in SEQID NO: 11. Also provided by the invention is a coding sequence for amature polypeptide or a fragment thereof, by itself as well as a codingsequence for a mature polypeptide or a fragment in reading frame withanother coding sequence, such as a sequence encoding a leader orsecretory sequence, a pre-, or pro- or prepro-protein sequence. Thepolynucleotide of the invention may also contain at least one non-codingsequence, including for example, but not limited to at least onenon-coding 5′ and 3′ sequence, such as the transcribed butnon-translated sequences, termination signals (such as rho-dependent andrho-independent termination signals), ribosome binding sites, Kozaksequences, sequences that stabilize mRNA, introns, and polyadenylationsignals. The polynucleotide sequence may also comprise additional codingsequence encoding additional amino acids. For example, a marker sequencethat facilitates purification of the fused polypeptide can be encoded.In certain embodiments of the invention, the marker sequence is ahexa-histidine peptide (SEQ ID NO: 12), as provided in the pQE vector(Qiagen, Inc.) and described in Gentz et al., Proc. Natl. Acad. Sci.,USA 86: 821-824 (1989), or an HA peptide tag (Wilson et al., Cell 37:767 (1984), both of which may be useful in purifying polypeptidesequence fused to them. Polynucleotides of the invention also include,but are not limited to, polynucleotides comprising a structural gene andits naturally associated sequences that control gene expression.

The nucleotide sequence encoding the Protein E polypeptide of SEQ ID NO:1-10 may be identical to the corresponding polynucleotide encodingsequence of SEQ ID NO: 11 (or comprised within SEQ ID NO: 11).Alternatively it may be any sequence, which as a result of theredundancy (degeneracy) of the genetic code, also encodes a polypeptideof SEQ ID NO: 1-10.

The term “polynucleotide encoding a polypeptide” as used hereinencompasses polynucleotides that include a sequence encoding apolypeptide of the invention, particularly a bacterial polypeptide andmore particularly a polypeptide of the non typeable H. influenzaeProtein E having an amino acid sequence set out in any of the sequencesof SEQ ID NO: 1-10 or fragments thereof. The term also encompassespolynucleotides that include a single continuous region or discontinuousregions encoding the polypeptide (for example, polynucleotidesinterrupted by integrated phage, an integrated insertion sequence, anintegrated vector sequence, an integrated transposon sequence, or due toRNA editing or genomic DNA reorganization) together with additionalregions, that also may contain coding and/or non-coding sequences.

The invention further relates to variants of the polynucleotidesdescribed herein that encode variants of a polypeptide having a deducedamino acid sequence of any of the sequences of SEQ ID NO: 1-10.Fragments of polynucleotides of the invention may be used, for example,to synthesize full-length polynucleotides of the invention.

Preferred fragments are those polynucleotides which encode a B-cellepitope, for example the fragments/peptides described in Example 10, andrecombinant, chimeric genes comprising said polynucleotide fragments.

Further particularly preferred embodiments are polynucleotides encodingProtein E variants, that have the amino acid sequence of Protein Epolypeptide of any sequence from SEQ ID NO: 1-10 in which several, afew, 5 to 10, 1 to 5, 1 to 3, 2, 1 or no amino acid residues aresubstituted, modified, deleted and/or added, in any combination.Especially preferred among these are silent substitutions, additions anddeletions, that do not alter the properties and activities of Protein Epolypeptide (for instance those properties described in the Examplesection herein).

Further preferred embodiments of the invention are polynucleotides thatare at least 85% identical over their entire length to polynucleotidesencoding Protein E polypeptides having an amino acid sequence set out inany of the sequences of SEQ ID NO: 1-10, and polynucleotides that arecomplementary to such polynucleotides. Alternatively, most highlypreferred are polynucleotides that comprise a region that is at least90% identical over its entire length to polynucleotides encoding ProteinE polypeptides and polynucleotides complementary thereto. In thisregard, polynucleotides at least 95% identical over their entire lengthto the same are particularly preferred. Furthermore, those with at least97% are highly preferred among those with at least 95%, and among thesethose with at least 98% and at least 99% are particularly highlypreferred, with at least 99% being the more preferred.

Preferred embodiments are polynucleotides encoding polypeptides thatretain substantially the same biological function or activity as themature polypeptide encoded by a DNA sequence selected from SEQ ID NO: 11(for instance those activities described in the Example section herein).

In accordance with certain preferred embodiments of this invention thereare provided polynucleotides that hybridize, particularly understringent conditions, to Protein E polynucleotide sequences, such asthose polynucleotides of SEQ ID NO: 11.

The invention further relates to polynucleotides that hybridize to thepolynucleotide sequences provided herein. In this regard, the inventionespecially relates to polynucleotides that hybridize under stringentconditions to the polynucleotides described herein. As herein used, theterms “stringent conditions” and “stringent hybridization conditions”mean hybridization occurring only if there is at least 95% andpreferably at least 97% identity between the sequences. A specificexample of stringent hybridization conditions is overnight incubation at42° C. in a solution comprising: 50% formamide, 5×SSC (150 mM NaCl, 15mM trisodium citrate), 50 mM sodium phosphate (pH7.6), 5× Denhardt'ssolution, 10% dextran sulfate, and 20 micrograms/ml of denatured,sheared salmon sperm DNA, followed by washing the hybridization supportin 0.1×SSC at about 65° C. Hybridization and wash conditions are wellknown and exemplified in Sambrook, et al., Molecular Cloning: ALaboratory Manual, Second Edition, Cold Spring Harbor, N.Y., (1989),particularly Chapter 11 therein. Solution hybridization may also be usedwith the polynucleotide sequences provided by the invention.

The invention also provides a polynucleotide consisting of or comprisinga polynucleotide sequence obtained by screening an appropriate librarycontaining the complete gene for a polynucleotide sequence set forth inany of the sequences of SEQ ID NO: 11 under stringent hybridizationconditions with a probe having the sequence of said polynucleotidesequence set forth in the corresponding sequence of SEQ ID NO: 11 or afragment thereof; and isolating said polynucleotide sequence. Fragmentsuseful for obtaining such a polynucleotide include, for example, probesand primers fully described elsewhere herein.

As discussed elsewhere herein regarding polynucleotide assays of theinvention, for instance, the polynucleotides of the invention, may beused as a hybridization probe for RNA, cDNA and genomic DNA to isolatefull-length cDNAs and genomic clones encoding Protein E and to isolatecDNA and genomic clones of other genes that have a high identity,particularly high sequence identity, to the Protein E genes. Such probesgenerally will comprise at least 15 nucleotide residues or base pairs.Preferably, such probes will have at least 30 nucleotide residues orbase pairs and may have at least 50 nucleotide residues or base pairs.Particularly preferred probes will have at least 20 nucleotide residuesor base pairs and will have less than 30 nucleotide residues or basepairs.

A coding region of Protein E genes may be isolated by screening using aDNA sequence provided in SEQ ID NO: 11 to synthesize an oligonucleotideprobe. A labeled oligonucleotide having a sequence complementary to thatof a gene of the invention is then used to screen a library of cDNA,genomic DNA or mRNA to determine which members of the library the probehybridizes to.

There are several methods available and well known to those skilled inthe art to obtain full-length DNAs, or extend short DNAs, for examplethose based on the method of Rapid Amplification of cDNA ends (RACE)(see, for example, Frohman, et al., PNAS USA 85: 8998-9002, 1988).Recent modifications of the technique, exemplified by the Marathon™technology (Clontech Laboratories Inc.) for example, have significantlysimplified the search for longer cDNAs. In the Marathon™ technology,cDNAs have been prepared from mRNA extracted from a chosen tissue and an‘adaptor’ sequence ligated onto each end. Nucleic acid amplification(PCR) is then carried out to amplify the “missing” 5′ end of the DNAusing a combination of gene specific and adaptor specificoligonucleotide primers. The PCR reaction is then repeated using“nested” primers, that is, primers designed to anneal within theamplified product (typically an adaptor specific primer that annealsfurther 3′ in the adaptor sequence and a gene specific primer thatanneals further 5′ in the selected gene sequence). The products of thisreaction can then be analyzed by DNA sequencing and a full-length DNAconstructed either by joining the product directly to the existing DNAto give a complete sequence, or carrying out a separate full-length PCRusing the new sequence information for the design of the 5′ primer.

The polynucleotides and polypeptides of the invention may be employed,for example, as research reagents and materials for discovery oftreatments of and diagnostics for diseases, particularly human diseases,as further discussed herein relating to polynucleotide assays.

The polynucleotides of the invention that are oligonucleotides derivedfrom a sequence of SEQ ID NO: 11 may be used in the processes herein asdescribed, but preferably for PCR, to determine whether or not thepolynucleotides identified herein in whole or in part are transcribed inbacteria in infected tissue. It is recognized that such sequences willalso have utility in diagnosis of the stage of infection and type ofinfection the pathogen has attained.

The invention also provides polynucleotides that encode a polypeptidethat is the mature protein plus additional amino or carboxyl-terminalamino acids, or amino acids interior to the mature polypeptide (when themature form has more than one polypeptide chain, for instance). Suchsequences may play a role in processing of a protein from precursor to amature form, may allow protein transport, may lengthen or shortenprotein half-life or may facilitate manipulation of a protein for assayor production, among other things. As generally is the case in vivo, theadditional amino acids may be processed away from the mature protein bycellular enzymes.

For each and every polynucleotide of the invention there is provided apolynucleotide complementary to it. It is preferred that thesecomplementary polynucleotides are fully complementary to eachpolynucleotide with which they are complementary.

A precursor protein, having a mature form of the polypeptide fused toone or more prosequences may be an inactive form of the polypeptide.When prosequences are removed such inactive precursors generally areactivated. Some or all of the prosequences may be removed beforeactivation. Generally, such precursors are called proproteins.

In addition to the standard A, G, C, T/U representations fornucleotides, the term “N” may also be used in describing certainpolynucleotides of the invention. “N” means that any of the four DNA orRNA nucleotides may appear at such a designated position in the DNA orRNA sequence, except it is preferred that N is not a nucleic acid thatwhen taken in combination with adjacent nucleotide positions, when readin the correct reading frame, would have the effect of generating apremature termination codon in such reading frame.

In sum, a polynucleotide of the invention may encode a mature protein, amature protein plus a leader sequence (which may be referred to as apreprotein), a precursor of a mature protein having one or moreprosequences that are not the leader sequences of a preprotein, or apreproprotein, which is a precursor to a proprotein, having a leadersequence and one or more prosequences, which generally are removedduring processing steps that produce active and mature forms of thepolypeptide.

In accordance with an aspect of the invention, there is provided the useof a polynucleotide of the invention for therapeutic or prophylacticpurposes, in particular genetic immunization.

The use of a polynucleotide of the invention in genetic immunizationwill preferably employ a suitable delivery method such as directinjection of plasmid DNA into muscles (Wolff et al., Hum Mol Genet(1992) 1: 363, Manthorpe et al., Hum. Gene Ther. (1983) 4: 419),delivery of DNA complexed with specific protein carriers (Wu et al., JBiol Chem. (1989) 264: 16985), coprecipitation of DNA with calciumphosphate (Benvenisty & Reshef, PNAS USA, (1986) 83: 9551),encapsulation of DNA in various forms of liposomes (Kaneda et al.,Science (1989) 243: 375), particle bombardment (Tang et al., Nature(1992) 356:152, Eisenbraun et al., DNA Cell Biol (1993) 12: 791) and invivo infection using cloned retroviral vectors (Seeger et al., PNAS USA(1984) 81: 5849).

Vectors, Host Cells, Expression Systems

The invention also relates to vectors that comprise a polynucleotide orpolynucleotides of the invention, host cells that are geneticallyengineered with vectors of the invention and the production ofpolypeptides of the invention by recombinant techniques. Cell-freetranslation systems can also be employed to produce such proteins usingRNAs derived from the DNA constructs of the invention.

Recombinant polypeptides of the present invention may be prepared byprocesses well known in those skilled in the art from geneticallyengineered host cells comprising expression systems. Accordingly, in afurther aspect, the present invention relates to expression systems thatcomprise a polynucleotide or polynucleotides of the present invention,to host cells which are genetically engineered with such expressionsystems, and to the production of polypeptides of the invention byrecombinant techniques.

For recombinant production of the polypeptides of the invention, hostcells can be genetically engineered to incorporate expression systems orportions thereof or polynucleotides of the invention. Introduction of apolynucleotide into the host cell can be effected by methods describedin many standard laboratory manuals, such as Davis, et al., BASICMETHODS IN MOLECULAR BIOLOGY, (1986) and Sambrook, et al., MOLECULARCLONING: A LABORATORY MANUAL, 2nd Ed., Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y. (1989), such as, calcium phosphatetransfection, DEAE-dextran mediated transfection, transvection,microinjection, cationic lipid-mediated transfection, electroporation,conjugation, transduction, scrape loading, ballistic introduction andinfection.

Representative examples of appropriate hosts include bacterial cells,such as cells of streptococci, staphylococci, enterococci, E. coli,streptomyces, cyanobacteria, Bacillus subtilis, Neisseria meningitidis,Haemophilus influenzae and Moraxella catarrhalis; fungal cells, such ascells of a yeast, Kluveromyces, Saccharomyces, Pichia, a basidiomycete,Candida albicans and Aspergillus; insect cells such as cells ofDrosophila S2 and Spodoptera Sf9; animal cells such as CHO, COS, HeLa,C127, 3T3, BHK, 293, CV-1 and Bowes melanoma cells; and plant cells,such as cells of a gymnosperm or angiosperm.

A great variety of expression systems can be used to produce thepolypeptides of the invention. Such vectors include, among others,chromosomal-, episomal- and virus-derived vectors, for example, vectorsderived from bacterial plasmids, from bacteriophage, from transposons,from yeast episomes, from insertion elements, from yeast chromosomalelements, from viruses such as baculoviruses, papova viruses, such asSV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabiesviruses, picornaviruses, retroviruses, and alphaviruses and vectorsderived from combinations thereof, such as those derived from plasmidand bacteriophage genetic elements, such as cosmids and phagemids. Theexpression system constructs may contain control regions that regulateas well as engender expression. Generally, any system or vector suitableto maintain, propagate or express polynucleotides and/or to express apolypeptide in a host may be used for expression in this regard. Theappropriate DNA sequence may be inserted into the expression system byany of a variety of well-known and routine techniques, such as, forexample, those set forth in Sambrook et al., MOLECULAR CLONING, ALABORATORY MANUAL, (supra).

In recombinant expression systems in eukaryotes, for secretion of atranslated protein into the lumen of the endoplasmic reticulum, into theperiplasmic space or into the extracellular environment, appropriatesecretion signals may be incorporated into the expressed polypeptide.These signals may be endogenous to the polypeptide or they may beheterologous signals.

Polypeptides of the present invention can be recovered and purified fromrecombinant cell cultures by well-known methods including ammoniumsulfate or ethanol precipitation, acid extraction, anion or cationexchange chromatography, phosphocellulose chromatography, hydrophobicinteraction chromatography, affinity chromatography, hydroxylapatitechromatography and lectin chromatography. Most preferably, ion metalaffinity chromatography (IMAC) is employed for purification. Well knowntechniques for refolding proteins may be employed to regenerate activeconformation when the polypeptide is denatured during intracellularsynthesis, isolation and or purification.

The expression system may also be a recombinant live microorganism, suchas a virus or bacterium. The gene of interest can be inserted into thegenome of a live recombinant virus or bacterium. Inoculation and in vivoinfection with this live vector will lead to in vivo expression of theantigen and induction of immune responses. Viruses and bacteria used forthis purpose are for instance: poxviruses (e.g; vaccinia, fowlpox,canarypox), alphaviruses (Sindbis virus, Semliki Forest Virus,Venezuelian Equine Encephalitis Virus), adenoviruses, adeno-associatedvirus, picornaviruses (poliovirus, rhinovirus), herpesviruses (varicellazoster virus, etc), Listeria, Salmonella, Shigella, BCG, streptococci.These viruses and bacteria can be virulent, or attenuated in variousways in order to obtain live vaccines. Such live vaccines also form partof the invention.

Diagnostic, Prognostic, Serotyping and Mutation Assays

This invention is also related to the use of Protein E polynucleotidesand polypeptides of the invention for use as diagnostic reagents.Detection of Protein E polynucleotides and/or polypeptides in aeukaryote, particularly a mammal, and especially a human, will provide adiagnostic method for diagnosis of disease, staging of disease orresponse of an infectious organism to drugs. Eukaryotes, particularlymammals, and especially humans, particularly those infected or suspectedto be infected with an organism comprising the Protein E genes orproteins, may be detected at the nucleic acid or amino acid level by avariety of well known techniques as well as by methods provided herein.

Polypeptides and polynucleotides for prognosis, diagnosis or otheranalysis may be obtained from a putatively infected and/or infectedindividual's bodily materials. Polynucleotides from any of thesesources, particularly DNA or RNA, may be used directly for detection ormay be amplified enzymatically by using PCR or any other amplificationtechnique prior to analysis. RNA, particularly mRNA, cDNA and genomicDNA may also be used in the same ways. Using amplification,characterization of the species and strain of infectious or residentorganism present in an individual, may be made by an analysis of thegenotype of a selected polynucleotide of the organism. Deletions andinsertions can be detected by a change in size of the amplified productin comparison to a genotype of a reference sequence selected from arelated organism, preferably a different species of the same genus or adifferent strain of the same species. Point mutations can be identifiedby hybridizing amplified DNA to labeled Protein E polynucleotidesequences. Perfectly or significantly matched sequences can bedistinguished from imperfectly or more significantly mismatched duplexesby DNase or RNase digestion, for DNA or RNA respectively, or bydetecting differences in melting temperatures or renaturation kinetics.Polynucleotide sequence differences may also be detected by alterationsin the electrophoretic mobility of polynucleotide fragments in gels ascompared to a reference sequence. This may be carried out with orwithout denaturing agents. Polynucleotide differences may also bedetected by direct DNA or RNA sequencing. See, for example, Myers etal., Science, 230: 1242 (1985). Sequence changes at specific locationsalso may be revealed by nuclease protection assays, such as RNase, V1and S1 protection assay or a chemical cleavage method. See, for example,Cotton et al., Proc. Natl. Acad. Sci., USA, 85: 4397-4401 (1985).

In another embodiment, an array of oligonucleotides probes comprisingProtein E nucleotide sequences or fragments thereof can be constructedto conduct efficient screening of, for example, genetic mutations,serotype, taxonomic classification or identification. Array technologymethods are well known and have general applicability and can be used toaddress a variety of questions in molecular genetics including geneexpression, genetic linkage, and genetic variability (see, for example,Chee et al., Science, 274: 610 (1996)).

Thus in another aspect, the present invention relates to a diagnostickit which comprises:

-   (a) a polynucleotide of the present invention, preferably any of the    nucleotide sequences of SEQ ID NO: 11, or a fragment thereof;-   (b) a nucleotide sequence complementary to that of (a);-   (c) a polypeptide of the present invention, preferably any of the    polypeptides of SEQ ID NO: 1-10 or a fragment thereof; or-   (d) an antibody to a polypeptide of the present invention,    preferably to any of the polypeptides of SEQ ID NO: 1-10.-   It will be appreciated that in any such kit, (a), (b), (c) or (d)    may comprise a substantial component. Such a kit will be of use in    diagnosing a disease or susceptibility to a Disease, among others.

This invention also relates to the use of polynucleotides of the presentinvention as diagnostic reagents. Detection of a mutated form of apolynucleotide of the invention, preferably any sequence of SEQ ID NO:11, which is associated with a disease or pathogenicity will provide adiagnostic tool that can add to, or define, a diagnosis of a disease, aprognosis of a course of disease, a determination of a stage of disease,or a susceptibility to a disease, which results from under-expression,over-expression or altered expression of the polynucleotide. Organisms,particularly infectious organisms, carrying mutations in suchpolynucleotide may be detected at the polynucleotide level by a varietyof techniques, such as those described elsewhere herein.

Cells from an organism carrying mutations or polymorphisms (allelicvariations) in a polynucleotide and/or polypeptide of the invention mayalso be detected at the polynucleotide or polypeptide level by a varietyof techniques, to allow for serotyping, for example. For example, RT-PCRcan be used to detect mutations in the RNA. It is particularly preferredto use RT-PCR in conjunction with automated detection systems, such as,for example, GeneScan. RNA, cDNA or genomic DNA may also be used for thesame purpose, PCR. As an example, PCR primers complementary to apolynucleotide encoding Protein E polypeptides can be used to identifyand analyze mutations.

The invention further provides primers with 1, 2, 3 or 4 nucleotidesremoved from the 5′ and/or the 3′ end. These primers may be used for,among other things, amplifying Protein E DNA and/or RNA isolated from asample derived from an individual, such as a bodily material. Theprimers may be used to amplify a polynucleotide isolated from aninfected individual, such that the polynucleotide may then be subject tovarious techniques for elucidation of the polynucleotide sequence. Inthis way, mutations in the polynucleotide sequence may be detected andused to diagnose and/or prognose the infection or its stage or course,or to serotype and/or classify the infectious agent.

The invention further provides a process for diagnosing, disease,preferably bacterial infections, more preferably infections caused bynon typeable H. influenzae, comprising determining from a sample derivedfrom an individual, such as a bodily material, an increased level ofexpression of polynucleotide having a sequence of any of the sequencesof SEQ ID NO: 11. Increased or decreased expression of Protein Epolynucleotide can be measured using any on of the methods well known inthe art for the quantitation of polynucleotides, such as, for example,amplification, PCR, RT-PCR, RNase protection, Northern blotting,spectrometry and other hybridization methods. In addition, a diagnosticassay in accordance with the invention for detecting over-expression ofProtein E polypeptides compared to normal control tissue samples may beused to detect the presence of an infection, for example. Assaytechniques that can be used to determine levels of Protein Epolypeptides, in a sample derived from a host, such as a bodilymaterial, are well-known to those of skill in the art. Such assaymethods include radio-immunoassays, competitive-binding assays, WesternBlot analysis, antibody sandwich assays, antibody detection and ELISAassays.

The polynucleotides of the invention may be used as components ofpolynucleotide arrays, preferably high density arrays or grids. Thesehigh density arrays are particularly useful for diagnostic andprognostic purposes. For example, a set of spots each comprising adifferent gene, and further comprising a polynucleotide orpolynucleotides of the invention, may be used for probing, such as usinghybridization or nucleic acid amplification, using a probes obtained orderived from a bodily sample, to determine the presence of a particularpolynucleotide sequence or related sequence in an individual. Such apresence may indicate the presence of a pathogen, particularlynon-typeable H. influenzae, and may be useful in diagnosing and/orprognosing disease or a course of disease. A grid comprising a number ofvariants of any polynucleotide sequence of SEQ ID NO: 11 is preferred.Also preferred is a number of variants of a polynucleotide sequenceencoding any polypeptide sequence of SEQ ID NO: 1-10.

Antibodies

The polypeptides and polynucleotides of the invention or variantsthereof, or cells expressing the same can be used as immunogens toproduce antibodies immunospecific for such polypeptides orpolynucleotides respectively. Alternatively, mimotopes, particularlypeptide mimotopes, of epitopes within the polypeptide sequence may alsobe used as immunogens to produce antibodies immunospecific for thepolypeptide of the invention. The term “immunospecific” means that theantibodies have substantially greater affinity for the polypeptides ofthe invention than their affinity for other related polypeptides in theprior art.

In certain preferred embodiments of the invention there are providedantibodies against Protein E polypeptides or polynucleotides.

Antibodies generated against the polypeptides or polynucleotides of theinvention can be obtained by administering the polypeptides and/orpolynucleotides of the invention, or epitope-bearing fragments of eitheror both, analogues of either or both, or cells expressing either orboth, to an animal, preferably a nonhuman, using routine protocols. Forpreparation of monoclonal antibodies, any technique known in the artthat provides antibodies produced by continuous cell line cultures canbe used. Examples include various techniques, such as those in Kohler,G. and Milstein, C., Nature 256: 495-497 (1975); Kozbor et al.,Immunology Today 4: 72 (1983); Cole et al., pg. 77-96 in MONOCLONALANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc. (1985).

Techniques for the production of single chain antibodies (U.S. Pat. No.4,946,778) can be adapted to produce single chain antibodies topolypeptides or polynucleotides of this invention. Also, transgenicmice, or other organisms or animals, such as other mammals, may be usedto express humanized antibodies immunospecific to the polypeptides orpolynucleotides of the invention.

Alternatively, phage display technology may be utilized to selectantibody genes with binding activities towards a polypeptide of theinvention either from repertoires of PCR amplified v-genes oflymphocytes from humans screened for possessing anti-Protein E or fromnaive libraries (McCafferty, et al., (1990), Nature 348, 552-554; Marks,et al., (1992) Biotechnology 10, 779-783). The affinity of theseantibodies can also be improved by, for example, chain shuffling(Clackson et al., (1991) Nature 352: 628).

The above-described antibodies may be employed to isolate or to identifyclones expressing the polypeptides or polynucleotides of the inventionto purify the polypeptides or polynucleotides by, for example, affinitychromatography.

Thus, among others, antibodies against Protein E polypeptides or ProteinE polynucleotides may be employed to treat infections, particularlybacterial infections.

Polypeptide variants include antigenically, epitopically orimmunologically equivalent variants form a particular aspect of thisinvention.

Preferably, the antibody or variant thereof is modified to make it lessimmunogenic in the individual. For example, if the individual is humanthe antibody may most preferably be “humanized,” where thecomplimentarity determining region or regions of the hybridoma-derivedantibody has been transplanted into a human monoclonal antibody, forexample as described in Jones et al. (1986), Nature 321, 522-525 orTempest et al., (1991) Biotechnology 9, 266-273.

Antagonists and Agonists—Assays and Molecules

Polypeptides and polynucleotides of the invention may also be used toassess the binding of small molecule substrates and ligands in, forexample, cells, cell-free preparations, chemical libraries, and naturalproduct mixtures. These substrates and ligands may be natural substratesand ligands or may be structural or functional mimetics. See, e.g.,Coligan et al., Current Protocols in Immunology 1(2): Chapter 5 (1991).

The screening methods may simply measure the binding of a candidatecompound to the polypeptide or polynucleotide, or to cells or membranesbearing the polypeptide or polynucleotide, or a fusion protein of thepolypeptide by means of a label directly or indirectly associated withthe candidate compound. Alternatively, the screening method may involvecompetition with a labeled competitor. Further, these screening methodsmay test whether the candidate compound results in a signal generated byactivation or inhibition of the polypeptide or polynucleotide, usingdetection systems appropriate to the cells comprising the polypeptide orpolynucleotide. Inhibitors of activation are generally assayed in thepresence of a known agonist and the effect on activation by the agonistby the presence of the candidate compound is observed. Constitutivelyactive polypeptide and/or constitutively expressed polypeptides andpolynucleotides may be employed in screening methods for inverseagonists or inhibitors, in the absence of an agonist or inhibitor, bytesting whether the candidate compound results in inhibition ofactivation of the polypeptide or polynucleotide, as the case may be.Further, the screening methods may simply comprise the steps of mixing acandidate compound with a solution containing a polypeptide orpolynucleotide of the present invention, to form a mixture, measuringProtein E polypeptides and/or polynucleotides activity in the mixture,and comparing the Protein E polypeptides and/or polynucleotides activityof the mixture to a standard. Fusion proteins, such as those made fromFc portion and Protein E polypeptides, as hereinbefore described, canalso be used for high-throughput screening assays to identifyantagonists of the polypeptide of the present invention, as well as ofphylogenetically and and/or functionally related polypeptides (see D.Bennett et al., J Mol Recognition, 8:52-58 (1995); and K. Johanson etal., J Biol Chem, 270(16):9459-9471 (1995)).

The polynucleotides, polypeptides and antibodies that bind to and/orinteract with a polypeptide of the present invention may also be used toconfigure screening methods for detecting the effect of added compoundson the production of mRNA and/or polypeptide in cells. For example, anELISA assay may be constructed for measuring secreted or cell associatedlevels of polypeptide using monoclonal and polyclonal antibodies bystandard methods known in the art. This can be used to discover agentswhich may inhibit or enhance the production of polypeptide (also calledantagonist or agonist, respectively) from suitably manipulated cells ortissues.

The invention also provides a method of screening compounds to identifythose which enhance (agonist) or block (antagonist) the action ofProtein E polypeptides or polynucleotides, particularly those compoundsthat are bacteriostatic and/or bactericidal. The method of screening mayinvolve high-throughput techniques. For example, to screen for agonistsor antagonists, a synthetic reaction mix, a cellular compartment, suchas a membrane, cell envelope or cell wall, or a preparation of anythereof, comprising Protein E polypeptides and a labeled substrate orligand of such polypeptide is incubated in the absence or the presenceof a candidate molecule that may be a Protein E agonist or antagonist.The ability of the candidate molecule to agonize or antagonize theProtein E polypeptide is reflected in decreased binding of the labeledligand or decreased production of product from such substrate. Moleculesthat bind gratuitously, i.e., without inducing the effects of Protein Epolypeptide are most likely to be good antagonists. Molecules that bindwell and, as the case may be, increase the rate of product productionfrom substrate, increase signal transduction, or increase chemicalchannel activity are agonists. Detection of the rate or level of, as thecase may be, production of product from substrate, signal transduction,or chemical channel activity may be enhanced by using a reporter system.Reporter systems that may be useful in this regard include but are notlimited to colorimetric, labeled substrate converted into product, areporter gene that is responsive to changes in Protein E polynucleotideor polypeptide activity, and binding assays known in the art.

Another example of an assay for Protein E agonists is a competitiveassay that combines Protein E and a potential agonist with Protein Ebinding molecules, recombinant Protein E binding molecules, naturalsubstrates or ligands, or substrate or ligand mimetics, underappropriate conditions for a competitive inhibition assay. Protein E canbe labeled, such as by radioactivity or a colorimetric compound, suchthat the number of Protein E molecules bound to a binding molecule orconverted to product can be determined accurately to assess theeffectiveness of the potential antagonist.

Potential antagonists include, among others, small organic molecules,peptides, polypeptides and antibodies that bind to a polynucleotideand/or polypeptide of the invention and thereby inhibit or extinguishits activity or expression. Potential antagonists also may be smallorganic molecules, a peptide, a polypeptide such as a closely relatedprotein or antibody that binds the same sites on a binding molecule,such as a binding molecule, without inducing Protein E inducedactivities, thereby preventing the action or expression of Protein Epolypeptides and/or polynucleotides by excluding Protein E polypeptidesand/or polynucleotides from binding.

Potential antagonists include a small molecule that binds to andoccupies the binding site of the polypeptide thereby preventing bindingto cellular binding molecules, such that normal biological activity isprevented. Examples of small molecules include but are not limited tosmall organic molecules, peptides or peptide-like molecules. Otherpotential antagonists include antisense molecules (see Okano, J.Neurochem. 56: 560 (1991); OLIGODEOXY-NUCLEOTIDES AS ANTISENSEINHIBITORS OF GENE EXPRESSION, CRC Press, Boca Raton, Fla. (1988), for adescription of these molecules). Preferred potential antagonists includecompounds related to and variants of Protein E.

In a further aspect, the present invention relates to geneticallyengineered soluble fusion proteins comprising a polypeptide of thepresent invention, or a fragment thereof, and various portions of theconstant regions of heavy or light chains of immunoglobulins of varioussub-classes (IgG, IgM, IgA, IgE). Preferred as an immunoglobulin is theconstant part of the heavy chain of human IgG, particularly IgG1, wherefusion takes place at the hinge region. In a particular embodiment, theFc part can be removed simply by incorporation of a cleavage sequencewhich can be cleaved with blood clotting factor Xa. Furthermore, thisinvention relates to processes for the preparation of these fusionproteins by genetic engineering, and to the use thereof for drugscreening, diagnosis and therapy. A further aspect of the invention alsorelates to polynucleotides encoding such fusion proteins. Examples offusion protein technology can be found in International PatentApplication Nos. WO94/29458 and WO94/22914.

Each of the polynucleotide sequences provided herein may be used in thediscovery and development of antibacterial compounds. The encodedprotein, upon expression, can be used as a target for the screening ofantibacterial drugs. Additionally, the polynucleotide sequences encodingthe amino terminal regions of the encoded protein or Shine-Delgarno orother translation facilitating sequences of the respective mRNA can beused to construct antisense sequences to control the expression of thecoding sequence of interest.

The invention also provides the use of the polypeptide, polynucleotide,agonist or antagonist of the invention to interfere with the initialphysical interaction between a pathogen or pathogens and a eukaryotic,preferably mammalian, host responsible for sequelae of infection. Inparticular, the molecules of the invention may be used: in theprevention of adhesion of bacteria, in particular gram positive and/orgram negative bacteria, to eukaryotic, preferably mammalian,extracellular matrix proteins on in-dwelling devices or to extracellularmatrix proteins in wounds; to block bacterial adhesion betweeneukaryotic, preferably mammalian, extracellular matrix proteins andbacterial Protein E proteins that mediate tissue damage and/or; to blockthe normal progression of pathogenesis in infections initiated otherthan by the implantation of in-dwelling devices or by other surgicaltechniques.

In accordance with yet another aspect of the invention, there areprovided Protein E agonists and antagonists, preferably bacteristatic orbactericidal agonists and antagonists.

The antagonists and agonists of the invention may be employed, forinstance, to prevent, inhibit and/or treat diseases.

In a further aspect, the present invention relates to mimotopes of thepolypeptide of the invention. A mimotope is a peptide sequence,sufficiently similar to the native peptide (sequentially orstructurally), which is capable of being recognised by antibodies whichrecognise the native peptide; or is capable of raising antibodies whichrecognise the native peptide when coupled to a suitable carrier.

Peptide mimotopes may be designed for a particular purpose by addition,deletion or substitution of elected amino acids. Thus, the peptides maybe modified for the purposes of ease of conjugation to a proteincarrier. For example, it may be desirable for some chemical conjugationmethods to include a terminal cysteine. In addition it may be desirablefor peptides conjugated to a protein carrier to include a hydrophobicterminus distal from the conjugated terminus of the peptide, such thatthe free unconjugated end of the peptide remains associated with thesurface of the carrier protein. Thereby presenting the peptide in aconformation which most closely resembles that of the peptide as foundin the context of the whole native molecule. For example, the peptidesmay be altered to have an N-terminal cysteine and a C-terminalhydrophobic amidated tail. Alternatively, the addition or substitutionof a D-stereoisomer form of one or more of the amino acids (inversosequences) may be performed to create a beneficial derivative, forexample to enhance stability of the peptide. Mimotopes may also be retrosequences of the natural peptide sequences, in that the sequenceorientation is reversed. Mimotopes may also be retro-inverso incharacter. Retro, inverso and retro-inverso peptides are described in WO95/24916 and WO 94/05311.

Alternatively, peptide mimotopes may be identified using antibodieswhich are capable themselves of binding to the polypeptides of thepresent invention using techniques such as phage display technology (EP0 552 267 B1). This technique, generates a large number of peptidesequences which mimic the structure of the native peptides and are,therefore, capable of binding to anti-native peptide antibodies, but maynot necessarily themselves share significant sequence homology to thenative polypeptide.

Vaccines

Another aspect of the invention relates to a method for inducing animmunological response in an individual, particularly a mammal,preferably humans, which comprises inoculating the individual withProtein E polynucleotide and/or polypeptide, or a fragment or variantthereof, adequate to produce antibody and/or T cell immune response toprotect said individual from infection, particularly bacterial infectionand most particularly non typeable H. influenzae infection. Alsoprovided are methods whereby such immunological response slows bacterialreplication. Yet another aspect of the invention relates to a method ofinducing immunological response in an individual which comprisesdelivering to such individual a nucleic acid vector, sequence orribozyme to direct expression of Protein E polynucleotides and/orpolypeptides, or a fragment or a variant thereof, for expressing ProteinE polynucleotides and/or polypeptides, or a fragment or a variantthereof in vivo in order to induce an immunological response, such as,to produce antibody and/or T cell immune response, including, forexample, cytokine-producing T cells or cytotoxic T cells, to protectsaid individual, preferably a human, from disease, whether that diseaseis already established within the individual or not. One example ofadministering the gene is by accelerating it into the desired cells as acoating on particles or otherwise. Such nucleic acid vector may compriseDNA, RNA, a ribozyme, a modified nucleic acid, a DNA/RNA hybrid, aDNA-protein complex or an RNA-protein complex.

A further aspect of the invention relates to an immunologicalcomposition that when introduced into an individual, preferably a human,capable of having induced within it an immunological response, inducesan immunological response in such individual to a Protein Epolynucleotide and/or polypeptide encoded therefrom, wherein thecomposition comprises a recombinant Protein E polynucleotide and/orpolypeptide encoded therefrom and/or comprises DNA and/or RNA whichencodes and expresses an antigen of said Protein E polynucleotide,polypeptide encoded therefrom, or other polypeptide of the invention.The immunological response may be used therapeutically orprophylactically and may take the form of antibody immunity and/orcellular immunity, such as cellular immunity arising from CTL or CD4+ Tcells.

Protein E polypeptides or a fragment thereof may be fused withco-protein or chemical moiety which may or may not by itself produceantibodies, but which is capable of stabilizing the first protein andproducing a fused or modified protein which will have antigenic and/orimmunogenic properties, and preferably protective properties. Thus fusedrecombinant protein, preferably further comprises an antigenicco-protein, such as lipoprotein or protein D from Haemophilus influenzae(EP 594610), Glutathione-S-transferase (GST) or beta-galactosidase, orany other relatively large co-protein which solubilizes the protein andfacilitates production and purification thereof. Moreover, theco-protein may act as an adjuvant in the sense of providing ageneralized stimulation of the immune system of the organism receivingthe protein. The co-protein may be attached to either the amino- orcarboxy-terminus of the first protein.

In a vaccine composition according to the invention, a Protein Epolypeptides and/or polynucleotides, or a fragment, or a mimotope, or avariant thereof may be present in a vector, such as the live recombinantvectors described above for example live bacterial vectors.

Also suitable are non-live vectors for the Protein E polypeptides, forexample bacterial outer-membrane vesicles or “blebs”. OM blebs arederived from the outer membrane of the two-layer membrane ofGram-negative bacteria and have been documented in many Gram-negativebacteria (Zhou, L et al. 1998. FEMS Microbiol. Lett. 163:223-228)including C. trachomatis and C. psittaci. A non-exhaustive list ofbacterial pathogens reported to produce blebs also includes: Bordetellapertussis, Borrelia burgdorferi, Brucella melitensis, Brucella ovis,Esherichia coli, Haemophilus influenzae, Legionella pneumophila,Moraxella catarrhalis, Neisseria gonorrhoeae, Neisseria meningitidis,Pseudomonas aeruginosa and Yersinia enterocolitica.

Blebs have the advantage of providing outer-membrane proteins in theirnative conformation and are thus particularly useful for vaccines. Blebscan also be improved for vaccine use by engineering the bacterium so asto modify the expression of one or more molecules at the outer membrane.Thus for example the expression of a desired immunogenic protein at theouter membrane, such as the Protein E polypeptides, can be introduced orupregulated (e.g. by altering the promoter). Instead or in addition, theexpression of outer-membrane molecules which are either not relevant(e.g. unprotective antigens or immunodominant but variable proteins) ordetrimental (e.g. toxic molecules such as LPS, or potential inducers ofan autoimmune response) can be downregulated. These approaches arediscussed in more detail below.

The non-coding flanking regions of the Protein E genes containregulatory elements important in the expression of the gene. Thisregulation takes place both at the transcriptional and translationallevel. The sequence of these regions, either upstream or downstream ofthe open reading frame of the gene, can be obtained by DNA sequencing.This sequence information allows the determination of potentialregulatory motifs such as the different promoter elements, terminatorsequences, inducible sequence elements, repressors, elements responsiblefor phase variation, the shine-dalgarno sequence, regions with potentialsecondary structure involved in regulation, as well as other types ofregulatory motifs or sequences. This sequence is a further aspect of theinvention.

This sequence information allows the modulation of the naturalexpression of the Protein E genes. The upregulation of the geneexpression may be accomplished by altering the promoter, theshine-dalgarno sequence, potential repressor or operator elements, orany other elements involved. Likewise, downregulation of expression canbe achieved by similar types of modification.

Alternatively, by changing phase variation sequences, the expression ofthe gene can be put under phase variation control, or it may beuncoupled from this regulation. In another approach, the expression ofthe gene can be put under the control of one or more inducible elementsallowing regulated expression. Examples of such regulation include, butare not limited to, induction by temperature shift, addition of inductorsubstrates like selected carbohydrates or their derivatives, traceelements, vitamins, co-factors, metal ions, etc.

Such modifications as described above can be introduced by severaldifferent means. The modification of sequences involved in geneexpression can be carried out in vivo by random mutagenesis followed byselection for the desired phenotype. Another approach consists inisolating the region of interest and modifying it by random mutagenesis,or site-directed replacement, insertion or deletion mutagenesis. Themodified region can then be reintroduced into the bacterial genome byhomologous recombination, and the effect on gene expression can beassessed. In another approach, the sequence knowledge of the region ofinterest can be used to replace or delete all or part of the naturalregulatory sequences. In this case, the regulatory region targeted isisolated and modified so as to contain the regulatory elements fromanother gene, a combination of regulatory elements from different genes,a synthetic regulatory region, or any other regulatory region, or todelete selected parts of the wild-type regulatory sequences. Thesemodified sequences can then be reintroduced into the bacterium viahomologous recombination into the genome. A non-exhaustive list ofpreferred promoters that could be used for up-regulation of geneexpression includes the promoters porA, porB, lbpB, tbpB, p110, lst,hpuAB from N. meningitidis or N. gonorroheae; ompCD, copB, lbpB, ompE,UspA1; UspA2; TbpB from M. Catarrhalis; p1, p2, p4, p5, p6, lpD, tbpB,D15, Hia, Hmw1, Hmw2 from H. influenzae.

In one example, the expression of the gene can be modulated byexchanging its promoter with a stronger promoter (through isolating theupstream sequence of the gene, in vitro modification of this sequence,and reintroduction into the genome by homologous recombination).Upregulated expression can be obtained in both the bacterium as well asin the outer membrane vesicles shed (or made) from the bacterium.

In other examples, the described approaches can be used to generaterecombinant bacterial strains with improved characteristics for vaccineapplications. These can be, but are not limited to, attenuated strains,strains with increased expression of selected antigens, strains withknock-outs (or decreased expression) of genes interfering with theimmune response, strains with modulated expression of immunodominantproteins, strains with modulated shedding of outer-membrane vesicles.

Thus, also provided by the invention is a modified upstream region ofthe Protein E genes, which modified upstream region contains aheterologous regulatory element which alters the expression level of theProtein E proteins located at the outer membrane. The upstream regionaccording to this aspect of the invention includes the sequence upstreamof the Protein E genes. The upstream region starts immediately upstreamof the Protein E genes and continues usually to a position no more thanabout 1000 by upstream of the gene from the ATG start codon. In the caseof a gene located in a polycistronic sequence (operon) the upstreamregion can start immediately preceding the gene of interest, orpreceding the first gene in the operon. Preferably, a modified upstreamregion according to this aspect of the invention contains a heterologouspromotor at a position between 500 and 700 by upstream of the ATG.

The use of the disclosed upstream regions to upregulate the expressionof the Protein E genes, a process for achieving this through homologousrecombination (for instance as described in WO 01/09350 incorporated byreference herein), a vector comprising upstream sequence suitable forthis purpose, and a host cell so altered are all further aspects of thisinvention.

Thus, the invention provides a Protein E polypeptides, in a modifiedbacterial bleb. The invention further provides modified host cellscapable of producing the non-live membrane-based bleb vectors. Theinvention further provides nucleic acid vectors comprising the Protein Egenes having a modified upstream region containing a heterologousregulatory element.

Further provided by the invention are processes to prepare the hostcells and bacterial blebs according to the invention.

Also provided by this invention are compositions, particularly vaccinecompositions, and methods comprising the polypeptides and/orpolynucleotides of the invention and immunostimulatory DNA sequences,such as those described in Sato, Y. et al. Science 273: 352 (1996).

Also, provided by this invention are methods using the describedpolynucleotide or particular fragments thereof, which have been shown toencode non-variable regions of bacterial cell surface proteins, inpolynucleotide constructs used in such genetic immunization experimentsin animal models of infection with non typeable H. influenzae. Suchexperiments will be particularly useful for identifying protein epitopesable to provoke a prophylactic or therapeutic immune response. It isbelieved that this approach will allow for the subsequent preparation ofmonoclonal antibodies of particular value, derived from the requisiteorgan of the animal successfully resisting or clearing infection, forthe development of prophylactic agents or therapeutic treatments ofbacterial infection, particularly non typeable H. influenzae infection,in mammals, particularly humans.

The invention also includes a vaccine formulation which comprises animmunogenic recombinant polypeptide and/or polynucleotide of theinvention together with a suitable carrier, such as a pharmaceuticallyacceptable carrier. Since the polypeptides and polynucleotides may bebroken down in the stomach, each is preferably administeredparenterally, including, for example, administration that issubcutaneous, intramuscular, intravenous, or intradermal. Formulationssuitable for parenteral administration include aqueous and non-aqueoussterile injection solutions which may contain anti-oxidants, buffers,bacteriostatic compounds and solutes which render the formulationisotonic with the bodily fluid, preferably the blood, of the individual;and aqueous and non-aqueous sterile suspensions which may includesuspending agents or thickening agents. The formulations may bepresented in unit-dose or multi-dose containers, for example, sealedampoules and vials and may be stored in a freeze-dried conditionrequiring only the addition of the sterile liquid carrier immediatelyprior to use.

The vaccine formulation of the invention may also include adjuvantsystems for enhancing the immunogenicity of the formulation. Preferablythe adjuvant system raises preferentially a TH1 type of response.

An immune response may be broadly distinguished into two extremecatagories, being a humoral or cell mediated immune responses(traditionally characterised by antibody and cellular effectormechanisms of protection respectively). These categories of responsehave been termed TH1-type responses (cell-mediated response), andTH2-type immune responses (humoral response).

Extreme TH1-type immune responses may be characterrised by thegeneration of antigen specific, haplotype restricted cytotoxic Tlymphocytes, and natural killer cell responses. In mice TH1-typeresponses are often characterised by the generation of antibodies of theIgG2a subtype, whilst in the human these correspond to IgG1 typeantibodies. TH2-type immune responses are characterised by thegeneration of a broad range of immunoglobulin isotypes including in miceIgG1, IgA, and IgM.

It can be considered that the driving force behind the development ofthese two types of immune responses are cytokines. High levels ofTH1-type cytokines tend to favour the induction of cell mediated immuneresponses to the given antigen, whilst high levels of TH2-type cytokinestend to favour the induction of humoral immune responses to the antigen.

The distinction of TH1 and TH2-type immune responses is not absolute. Inreality an individual will support an immune response which is describedas being predominantly TH1 or predominantly TH2. However, it is oftenconvenient to consider the families of cytokines in terms of thatdescribed in murine CD4 +ve T cell clones by Mosmann and Coffman(Mosmann, T. R. and Coffman, R. L. (1989) TH1 and TH2 cells: differentpatterns of lymphokine secretion lead to different functionalproperties. Annual Review of Immunology, 7, p 145-173). Traditionally,TH1-type responses are associated with the production of the INF-γ andIL-2 cytokines by T-lymphocytes. Other cytokines often directlyassociated with the induction of TH1-type immune responses are notproduced by T-cells, such as IL-12. In contrast, TH2-type responses areassociated with the secretion of IL-4, IL-5, IL-6 and IL-13.

It is known that certain vaccine adjuvants are particularly suited tothe stimulation of either TH1 or TH2-type cytokine responses.Traditionally the best indicators of the TH1:TH2 balance of the immuneresponse after a vaccination or infection includes direct measurement ofthe production of TH1 or TH2 cytokines by T lymphocytes in vitro afterrestimulation with antigen, and/or the measurement of the IgG1:IgG2aratio of antigen specific antibody responses.

Thus, a TH1-type adjuvant is one which preferentially stimulatesisolated T-cell populations to produce high levels of TH1-type cytokineswhen re-stimulated with antigen in vitro, and promotes development ofboth CD8+ cytotoxic T lymphocytes and antigen specific immunoglobulinresponses associated with TH1-type isotype.

Adjuvants which are capable of preferential stimulation of the TH1 cellresponse are described in International Patent Application No. WO94/00153 and WO 95/17209.

3 De-O-acylated monophosphoryl lipid A (3D-MPL) is one such adjuvant.This is known from GB 2220211 (Ribi). Chemically it is a mixture of 3De-O-acylated monophosphoryl lipid A with 4, 5 or 6 acylated chains andis manufactured by Ribi Immunochem, Montana. A preferred form of 3De-O-acylated monophosphoryl lipid A is disclosed in European Patent 0689 454 B1 (SmithKline Beecham Biologicals SA).

Preferably, the particles of 3D-MPL are small enough to be sterilefiltered through a 0.22 micron membrane (European Patent number 0 689454).

3D-MPL will be present in the range of 10 μg-100 μg preferably 25-50 μgper dose wherein the antigen will typically be present in a range 2-50μg per dose.

Another preferred adjuvant comprises QS21, an Hplc purified non-toxicfraction derived from the bark of Quillaja Saponaria Molina. Optionallythis may be admixed with 3 De-O-acylated monophosphoryl lipid A(3D-MPL), optionally together with an carrier.

The method of production of QS21 is disclosed in U.S. Pat. No.5,057,540.

Non-reactogenic adjuvant formulations containing QS21 have beendescribed previously (WO 96/33739). Such formulations comprising QS21and cholesterol have been shown to be successful TH1 stimulatingadjuvants when formulated together with an antigen.

Further adjuvants which are preferential stimulators of TH1 cellresponse include immunomodulatory oligonucleotides, for exampleunmethylated CpG sequences as disclosed in WO 96/02555.

Combinations of different TH1 stimulating adjuvants, such as thosementioned hereinabove, are also contemplated as providing an adjuvantwhich is a preferential stimulator of TH1 cell response. For example,QS21 can be formulated together with 3D-MPL. The ratio of QS21:3D-MPLwill typically be in the order of 1:10 to 10:1; preferably 1:5 to 5:1and often substantially 1:1. The preferred range for optimal synergy is2.5 :1 to 1:13D-MPL: QS21.

Preferably a carrier is also present in the vaccine compositionaccording to the invention. The carrier may be an oil in water emulsion,or an aluminium salt, such as aluminium phosphate or aluminiumhydroxide.

A preferred oil-in-water emulsion comprises a metabolisible oil, such assqualene, alpha tocopherol and Tween 80. In a particularly preferredaspect the antigens in the vaccine composition according to theinvention are combined with QS21 and 3D-MPL in such an emulsion.Additionally the oil in water emulsion may contain span 85 and/orlecithin and/or tricaprylin. Typically for human administration QS21 and3D-MPL will be present in a vaccine in the range of 1 μg-200 μg, such as10-100 μg, preferably 10 μg-50 μg per dose. Typically the oil in waterwill comprise from 2 to 10% squalene, from 2 to 10% alpha tocopherol andfrom 0.3 to 3% tween 80. Preferably the ratio of squalene: alphatocopherol is equal to or less than 1 as this provides a more stableemulsion. Span 85 may also be present at a level of 1%. In some cases itmay be advantageous that the vaccines of the present invention willfurther contain a stabiliser.

Non-toxic oil in water emulsions preferably contain a non-toxic oil,e.g. squalane or squalene, an emulsifier, e.g. Tween 80, in an aqueouscarrier. The aqueous carrier may be, for example, phosphate bufferedsaline.

A particularly potent adjuvant formulation involving QS21, 3D-MPL andtocopherol in an oil in water emulsion is described in WO 95/17210.

While the invention has been described with reference to certain ProteinE polypeptides and polynucleotides, it is to be understood that thiscovers fragments of the naturally occurring polypeptides andpolynucleotides, and similar polypeptides and polynucleotides withadditions, deletions or substitutions which do not substantially affectthe immunogenic properties of the recombinant polypeptides orpolynucleotides. Preferred fragments/peptides are described in Example10.

The present invention also provides a polyvalent vaccine compositioncomprising a vaccine formulation of the invention in combination withother antigens, in particular antigens useful for treating otitis media.Such a poly-valent vaccine composition may include a TH-1 inducingadjuvant as hereinbefore described.

In a preferred embodiment, the polypeptides, fragments and immunogens ofthe invention are formulated with one or more of the following groups ofantigens: a) one or more pneumococcal capsular polysaccharides (eitherplain or conjugated to a carrier protein); b) one or more antigens thatcan protect a host against M. catarrhalis infection; c) one or moreprotein antigens that can protect a host against Streptococcuspneumoniae infection; d) one or more further non typeable Haemophilusinfluenzae protein antigens; e) one or more antigens that can protect ahost against RSV; and f) one or more antigens that can protect a hostagainst influenza virus. Combinations with: groups a) and b); b) and c);b), d), and a) and/or c); b), d), e), f), and a) and/or c) arepreferred. Such vaccines may be advantageously used as global otitismedia vaccines.

The pneumococcal capsular polysaccharide antigens are preferablyselected from serotypes 1, 2, 3, 4, 5, 6B, 7F, 8, 9N, 9V, 10A, 11A, 12F,14, 15B, 17F, 18C, 19A, 19F, 20, 22F, 23F and 33F (most preferably fromserotypes 1, 3, 4, 5, 6B, 7F, 9V, 14, 18C, 19F and 23F).

Preferred pneumococcal protein antigens are those pneumococcal proteinswhich are exposed on the outer surface of the pneumococcus (capable ofbeing recognised by a host's immune system during at least part of thelife cycle of the pneumococcus), or are proteins which are secreted orreleased by the pneumococcus. Most preferably, the protein is a toxin,adhesin, 2-component signal tranducer, or lipoprotein of Streptococcuspneumoniae, or fragments thereof. Particularly preferred proteinsinclude, but are not limited to: pneumolysin (preferably detoxified bychemical treatment or mutation) [Mitchell et al. Nucleic Acids Res. 1990Jul. 11; 18(13): 4010 “Comparison of pneumolysin genes and proteins fromStreptococcus pneumoniae types 1 and 2.”, Mitchell et al. BiochimBiophys Acta 1989 Jan. 23; 1007(1): 67-72 “Expression of the pneumolysingene in Escherichia coli: rapid purification and biologicalproperties.”, WO 96/05859 (A. Cyanamid), WO 90/06951 (Paton et al), WO99/03884 (NAVA)]; PspA and transmembrane deletion variants thereof (WO92/14488; WO 99/53940; U.S. Pat. No. 5,804,193—Briles et al.); PspC andtransmembrane deletion variants thereof (WO 99/53940; WO 97/09994—Brileset al); PsaA and transmembrane deletion variants thereof (Berry & Paton,Infect Immun 1996 December;64(12):5255-62 “Sequence heterogeneity ofPsaA, a 37-kilodalton putative adhesin essential for virulence ofStreptococcus pneumoniae”); pneumococcal choline binding proteins andtransmembrane deletion variants thereof; CbpA and transmembrane deletionvariants thereof (WO 97/41151; WO 99/51266);Glyceraldehyde-3-phosphate-dehydrogenase (Infect. Immun. 1996 64:3544);HSP70 (WO 96/40928); PcpA (Sanchez-Beato et al. FEMS Microbiol Lett1998, 164:207-14); M like protein, SB patent application No. EP 0837130;and adhesin 18627 (SB Patent application No. EP 0834568). Furtherpreferred pneumococcal protein antigens are those disclosed in WO98/18931, particularly those selected in WO 98/18930 and PCT/US99/30390.

Preferred Moraxella catarrhalis protein antigens which can be includedin a combination vaccine (especially for the prevention of otitis media)are: OMP106 [WO 97/41731 (Antex) & WO 96/34960 (PMC)]; OMP21; LbpA &/orLbpB [WO 98/55606 (PMC)]; TbpA &/or TbpB [WO 97/13785 & WO 97/32980(PMC)]; CopB [Helminen M E, et al. (1993) Infect. Immun. 61:2003-2010];UspA1 and/or UspA2 [WO 93/03761 (University of Texas)]; OmpCD; HasR(PCT/EP99/03824); PilQ (PCT/EP99/03823); OMP85 (PCT/EP00/01468); lipo06(GB 9917977.2); lipo10 (GB 9918208.1); lipo11 (GB 9918302.2); lipo18 (GB9918038.2); P6 (PCT/EP99/03038); D15 (PCT/EP99/03822); OmplA1(PCT/EP99/06781); Hly3 (PCT/EP99/03257); and OmpE.

Preferred further non-typeable Haemophilus influenzae protein antigenswhich can be included in a combination vaccine (especially for theprevention of otitis media) include: Fimbrin protein [(U.S. Pat. No.5,766,608—Ohio State Research Foundation)] and fusions comprisingpeptides therefrom [eg LB1(f) peptide fusions; U.S. Pat. No. 5,843,464(OSU) or WO 99/64067]; OMP26 [WO 97/01638 (Cortecs)]; P6 [EP 281673(State University of New York)]; protein D (EP 594610); TbpA and/orTbpB; Hia; Hsf; Hin47; Hif; Hmw1; Hmw2; Hmw3; Hmw4; Hap; D15 (WO94/12641); P2; P5 (WO 94/26304); NlpC2 (BASB205) [WO 02/30971]; Slp(BASB203) [WO 02/30960]; and iOMP1681 (BASB210) [WO 02/34772].

Preferred influenza virus antigens include whole, live or inactivatedvirus, split influenza virus, grown in eggs or MDCK cells, or Vero cellsor whole flu virosomes (as described by R. Gluck, Vaccine, 1992, 10,915-920) or purified or recombinant proteins thereof, such as HA, NP,NA, or M proteins, or combinations thereof.

Preferred RSV (Respiratory Syncytial Virus) antigens include the Fglycoprotein, the G glycoprotein, the HN protein, or derivativesthereof.

Compositions, Kits and Administration

In a further aspect of the invention there are provided compositionscomprising a Protein E polynucleotides and/or a Protein E polypeptidesfor administration to a cell or to a multicellular organism.

The invention also relates to compositions comprising a polynucleotideand/or a polypeptides discussed herein or their agonists or antagonists.The polypeptides and polynucleotides of the invention may be employed incombination with a non-sterile or sterile carrier or carriers for usewith cells, tissues or organisms, such as a pharmaceutical carriersuitable for administration to an individual. Such compositionscomprise, for instance, a media additive or a therapeutically effectiveamount of a polypeptide and/or polynucleotide of the invention and apharmaceutically acceptable carrier or excipient. Such carriers mayinclude, but are not limited to, saline, buffered saline, dextrose,water, glycerol, ethanol and combinations thereof. The formulationshould suit the mode of administration. The invention further relates todiagnostic and pharmaceutical packs and kits comprising one or morecontainers filled with one or more of the ingredients of theaforementioned compositions of the invention.

Polypeptides, polynucleotides and other compounds of the invention maybe employed alone or in conjunction with other compounds, such astherapeutic compounds.

The pharmaceutical compositions may be administered in any effective,convenient manner including, for instance, administration by topical,oral, anal, vaginal, intravenous, intraperitoneal, intramuscular,subcutaneous, intranasal or intradermal routes among others.

In therapy or as a prophylactic, the active agent may be administered toan individual as an injectable composition, for example as a sterileaqueous dispersion, preferably isotonic.

In a further aspect, the present invention provides for pharmaceuticalcompositions comprising a therapeutically effective amount of apolypeptide and/or polynucleotide, such as the soluble form of apolypeptide and/or polynucleotide of the present invention, agonist orantagonist peptide or small molecule compound, in combination with apharmaceutically acceptable carrier or excipient. Such carriers include,but are not limited to, saline, buffered saline, dextrose, water,glycerol, ethanol, and combinations thereof. The invention furtherrelates to pharmaceutical packs and kits comprising one or morecontainers filled with one or more of the ingredients of theaforementioned compositions of the invention. Polypeptides,polynucleotides and other compounds of the present invention may beemployed alone or in conjunction with other compounds, such astherapeutic compounds.

The composition will be adapted to the route of administration, forinstance by a systemic or an oral route. Preferred forms of systemicadministration include injection, typically by intravenous injection.Other injection routes, such as subcutaneous, intramuscular, orintraperitoneal, can be used. Alternative means for systemicadministration include transmucosal and transdermal administration usingpenetrants such as bile salts or fusidic acids or other detergents. Inaddition, if a polypeptide or other compounds of the present inventioncan be formulated in an enteric or an encapsulated formulation, oraladministration may also be possible. Administration of these compoundsmay also be topical and/or localized, in the form of salves, pastes,gels, solutions, powders and the like.

For administration to mammals, and particularly humans, it is expectedthat the daily dosage level of the active agent will be from 0.01 mg/kgto 10 mg/kg, typically around 1 mg/kg. The physician in any event willdetermine the actual dosage which will be most suitable for anindividual and will vary with the age, weight and response of theparticular individual. The above dosages are exemplary of the averagecase. There can, of course, be individual instances where higher orlower dosage ranges are merited, and such are within the scope of thisinvention.

The dosage range required depends on the choice of peptide, the route ofadministration, the nature of the formulation, the nature of thesubject's condition, and the judgment of the attending practitioner.Suitable dosages, however, are in the range of 0.1-100 μg/kg of subject.

A vaccine composition is conveniently in injectable form. Conventionaladjuvants may be employed to enhance the immune response. A suitableunit dose for vaccination is 0.5-5 microgram/kg of antigen, and suchdose is preferably administered 1-3 times and with an interval of 1-3weeks. With the indicated dose range, no adverse toxicological effectswill be observed with the compounds of the invention which wouldpreclude their administration to suitable individuals.

Wide variations in the needed dosage, however, are to be expected inview of the variety of compounds available and the differingefficiencies of various routes of administration. For example, oraladministration would be expected to require higher dosages thanadministration by intravenous injection. Variations in these dosagelevels can be adjusted using standard empirical routines foroptimization, as is well understood in the art.

Sequence Databases, Sequences in a Tangible Medium, and Algorithms

Polynucleotide and polypeptide sequences form a valuable informationresource with which to determine their 2- and 3-dimensional structuresas well as to identify further sequences of similar homology. Theseapproaches are most easily facilitated by storing the sequence in acomputer readable medium and then using the stored data in a knownmacromolecular structure program or to search a sequence database usingwell known searching tools, such as the GCG program package.

Also provided by the invention are methods for the analysis of charactersequences or strings, particularly genetic sequences or encoded proteinsequences. Preferred methods of sequence analysis include, for example,methods of sequence homology analysis, such as identity and similarityanalysis, DNA, RNA and protein structure analysis, sequence assembly,cladistic analysis, sequence motif analysis, open reading framedetermination, nucleic acid base calling, codon usage analysis, nucleicacid base trimming, and sequencing chromatogram peak analysis.

A computer based method is provided for performing homologyidentification. This method comprises the steps of: providing a firstpolynucleotide sequence comprising the sequence of a polynucleotide ofthe invention in a computer readable medium; and comparing said firstpolynucleotide sequence to at least one second polynucleotide orpolypeptide sequence to identify homology.

A computer based method is also provided for performing homologyidentification, said method comprising the steps of: providing a firstpolypeptide sequence comprising the sequence of a polypeptide of theinvention in a computer readable medium; and comparing said firstpolypeptide sequence to at least one second polynucleotide orpolypeptide sequence to identify homology.

All publications and references, including but not limited to patentsand patent applications, cited in this specification are hereinincorporated by reference in their entirety as if each individualpublication or reference were specifically and individually indicated tobe incorporated by reference herein as being fully set forth. Any patentapplication to which this application claims priority is alsoincorporated by reference herein in its entirety in the manner describedabove for publications and references.

Definitions

“Identity,” as known in the art, is a relationship between two or morepolypeptide sequences or two or more polynucleotide sequences, as thecase may be, as determined by comparing the sequences. In the art,“identity” also means the degree of sequence relatedness betweenpolypeptide or polynucleotide sequences, as the case may be, asdetermined by the match between strings of such sequences. “Identity”can be readily calculated by known methods, including but not limited tothose described in (Computational Molecular Biology, Lesk, A. M., ed.,Oxford University Press, New York, 1988; Biocomputing: Informatics andGenome Projects, Smith, D. W., ed., Academic Press, New York, 1993;Computer Analysis of Sequence Data, Part I, Griffin, A. M., and Griffin,H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis inMolecular Biology, von Heine, G., Academic Press, 1987; and SequenceAnalysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press,New York, 1991; and Carillo, H., and Lipman, D., SIAM J. Applied Math.,48: 1073 (1988). Methods to determine identity are designed to give thelargest match between the sequences tested. Moreover, methods todetermine identity are codified in publicly available computer programs.Computer program methods to determine identity between two sequencesinclude, but are not limited to, the GAP program in the GCG programpackage (Devereux, J., et al., Nucleic Acids Research 12(1): 387(1984)), BLASTP, BLASTN (Altschul, S. F. et al., J. Molec. Biol. 215:403-410 (1990), and FASTA (Pearson and Lipman Proc. Natl. Acad. Sci. USA85; 2444-2448 (1988). The BLAST family of programs is publicly availablefrom NCBI and other sources (BLAST Manual, Altschul, S., et al., NCBINLM NIH Bethesda, Md. 20894; Altschul, S., et al., J. Mol. Biol. 215:403-410 (1990). The well known Smith Waterman algorithm may also be usedto determine identity.

Parameters for polypeptide sequence comparison include the following:

-   Algorithm: Needleman and Wunsch, J. Mol Biol. 48: 443-453 (1970)-   Comparison matrix: BLOSSUM62 from Henikoff and Henikoff, Proc. Natl.    Acad. Sci. USA. 89:10915-10919 (1992)-   Gap Penalty: 8-   Gap Length Penalty: 2-   A program useful with these parameters is publicly available as the    “gap” program from Genetics Computer Group, Madison Wis. The    aforementioned parameters are the default parameters for peptide    comparisons (along with no penalty for end gaps).

Parameters for polynucleotide comparison include the following:

-   Algorithm: Needleman and Wunsch, J. Mol Biol. 48: 443-453 (1970)-   Comparison matrix: matches=+10, mismatch=0-   Gap Penalty: 50-   Gap Length Penalty: 3-   Available as: The “gap” program from Genetics Computer Group,    Madison Wis. These are the default parameters for nucleic acid    comparisons.

A preferred meaning for “identity” for polynucleotides and polypeptides,as the case may be, are provided in (1) and (2) below.

(1) Polynucleotide embodiments further include an isolatedpolynucleotide comprising a polynucleotide sequence having at least a50, 60, 70, 80, 85, 90, 95, 97 or 100% identity to the referencesequence of SEQ ID NO: 11, wherein said polynucleotide sequence may beidentical to the reference sequence of SEQ ID NO: 11 or may include upto a certain integer number of nucleotide alterations as compared to thereference sequence, wherein said alterations are selected from the groupconsisting of at least one nucleotide deletion, substitution, includingtransition and transversion, or insertion, and wherein said alterationsmay occur at the 5′ or 3′ terminal positions of the reference nucleotidesequence or anywhere between those terminal positions, interspersedeither individually among the nucleotides in the reference sequence orin one or more contiguous groups within the reference sequence, andwherein said number of nucleotide alterations is determined bymultiplying the total number of nucleotides in SEQ ID NO: 11 by theinteger defining the percent identity divided by 100 and thensubtracting that product from said total number of nucleotides in SEQ IDNO: 11, or:

n _(n) ≦x _(n)−(x _(n) ·y),

wherein n_(n) is the number of nucleotide alterations, x_(n) is thetotal number of nucleotides in SEQ ID NO: 11, y is 0.50 for 50%, 0.60for 60%, 0.70 for 70%, 0.80 for 80%, 0.85 for 85%, 0.90 for 90%, 0.95for 95%, 0.97 for 97% or 1.00 for 100%, and · is the symbol for themultiplication operator, and wherein any non-integer product of x_(n)and y is rounded down to the nearest integer prior to subtracting itfrom x_(n). Alterations of polynucleotide sequences encoding thepolypeptides of SEQ ID NO:1-10 may create nonsense, missense orframeshift mutations in this coding sequence and thereby alter thepolypeptide encoded by the polynucleotide following such alterations.

By way of example, a polynucleotide sequence of the present inventionmay be identical to the reference sequences of SEQ ID NO: 11, that is itmay be 100% identical, or it may include up to a certain integer numberof nucleic acid alterations as compared to the reference sequence suchthat the percent identity is less than 100% identity. Such alterationsare selected from the group consisting of at least one nucleic aciddeletion, substitution, including transition and transversion, orinsertion, and wherein said alterations may occur at the 5′ or 3′terminal positions of the reference polynucleotide sequence or anywherebetween those terminal positions, interspersed either individually amongthe nucleic acids in the reference sequence or in one or more contiguousgroups within the reference sequence. The number of nucleic acidalterations for a given percent identity is determined by multiplyingthe total number of nucleic acids in SEQ ID NO: 11 by the integerdefining the percent identity divided by 100 and then subtracting thatproduct from said total number of nucleic acids in SEQ ID NO: 11, or:

n _(n) ≦x _(n)−(x _(n) ·y),

wherein n_(n) is the number of nucleic acid alterations, x_(n) is thetotal number of nucleic acids in SEQ ID NO: 11, y is, for instance 0.70for 70%, 0.80 for 80%, 0.85 for 85% etc., · is the symbol for themultiplication operator, and wherein any non-integer product of x_(n)and y is rounded down to the nearest integer prior to subtracting itfrom x_(n).

(2) Polypeptide embodiments further include an isolated polypeptidecomprising a polypeptide having at least a 50, 60, 70, 80, 85, 90, 95,97 or 100% identity to the polypeptide reference sequence of SEQ IDNO:1-10, wherein said polypeptide sequence may be identical to thereference sequence of SEQ ID NO:1-10 or may include up to a certaininteger number of amino acid alterations as compared to the referencesequence, wherein said alterations are selected from the groupconsisting of at least one amino acid deletion, substitution, includingconservative and non-conservative substitution, or insertion, andwherein said alterations may occur at the amino- or carboxy-terminalpositions of the reference polypeptide sequence or anywhere betweenthose terminal positions, interspersed either individually among theamino acids in the reference sequence or in one or more contiguousgroups within the reference sequence, and wherein said number of aminoacid alterations is determined by multiplying the total number of aminoacids in SEQ ID NO:1-10 by the integer defining the percent identitydivided by 100 and then subtracting that product from said total numberof amino acids in SEQ ID NO:1-10, respectively, or:

n _(a) ≦x _(a)−(x _(a) ·y)

wherein n_(a) is the number of amino acid alterations, x_(a) is thetotal number of amino acids in SEQ ID NO:1-10, y is 0.50 for 50%, 0.60for 60%, 0.70 for 70%, 0.80 for 80%, 0.85 for 85%, 0.90 for 90%, 0.95for 95%, 0.97 for 97% or 1.00 for 100%, and · is the symbol for themultiplication operator, and wherein any non-integer product of x_(a)and y is rounded down to the nearest integer prior to subtracting itfrom x_(a).

By way of example, a polypeptide sequence of the present invention maybe identical to the reference sequence of SEQ ID NO:1-10, that is it maybe 100% identical, or it may include up to a certain integer number ofamino acid alterations as compared to the reference sequence such thatthe percent identity is less than 100% identity. Such alterations areselected from the group consisting of at least one amino acid deletion,substitution, including conservative and non-conservative substitution,or insertion, and wherein said alterations may occur at the amino- orcarboxy-terminal positions of the reference polypeptide sequence oranywhere between those terminal positions, interspersed eitherindividually among the amino acids in the reference sequence or in oneor more contiguous groups within the reference sequence. The number ofamino acid alterations for a given % identity is determined bymultiplying the total number of amino acids in SEQ ID NO:1-10 by theinteger defining the percent identity divided by 100 and thensubtracting that product from said total number of amino acids in SEQ IDNO:1-10, or:

n _(a) ≦x _(a)−(x _(a) ·y),

wherein n_(a) is the number of amino acid alterations, x_(a) is thetotal number of amino acids in SEQ ID NO:1-10, y is, for instance 0.70for 70%, 0.80 for 80%, 0.85 for 85% etc., and · is the symbol for themultiplication operator, and wherein any non-integer product of x_(a)and y is rounded down to the nearest integer prior to subtracting itfrom x_(a).

“Individual(s),” when used herein with reference to an organism, means amulticellular eukaryote, including, but not limited to a metazoan, amammal, an ovid, a bovid, a simian, a primate, and a human.

“Isolated” means altered by the hand of man” from its natural state,i.e., if it occurs in nature, it has been changed or removed from itsoriginal environment, or both. For example, a polynucleotide or apolypeptide naturally present in a living organism is not “isolated,”but the same polynucleotide or polypeptide separated from the coexistingmaterials of its natural state is “isolated”, as the term is employedherein. Moreover, a polynucleotide or polypeptide that is introducedinto an organism by transformation, genetic manipulation or by any otherrecombinant method is “isolated” even if it is still present in saidorganism, which organism may be living or non-living.

“Polynucleotide(s)” generally refers to any polyribonucleotide orpolydeoxyribonucleotide, which may be unmodified RNA or DNA or modifiedRNA or DNA including single and double-stranded regions.

“Variant” refers to a polynucleotide or polypeptide that differs from areference polynucleotide or polypeptide, but retains essentialproperties. A typical variant of a polynucleotide differs in nucleotidesequence from another, reference polynucleotide. Changes in thenucleotide sequence of the variant may or may not alter the amino acidsequence of a polypeptide encoded by the reference polynucleotide.Nucleotide changes may result in amino acid substitutions, additions,deletions, fusions and truncations in the polypeptide encoded by thereference sequence, as discussed below. A typical variant of apolypeptide differs in amino acid sequence from another, referencepolypeptide. Generally, differences are limited so that the sequences ofthe reference polypeptide and the variant are closely similar overalland, in many regions, identical. A variant and reference polypeptide maydiffer in amino acid sequence by one or more substitutions, additions,deletions in any combination. A substituted or inserted amino acidresidue may or may not be one encoded by the genetic code. A variant ofa polynucleotide or polypeptide may be a naturally occurring such as anallelic variant, or it may be a variant that is not known to occurnaturally. Non-naturally occurring variants of polynucleotides andpolypeptides may be made by mutagenesis techniques or by directsynthesis.

“Disease(s)” means any disease caused by or related to infection by abacteria, including, for example, otitis media in infants and children,pneumonia in elderlies, sinusitis, nosocomial infections and invasivediseases, chronic otitis media with hearing loss, fluid accumulation inthe middle ear, auditive nerve damage, delayed speech learning,infection of the upper respiratory tract and inflammation of the middleear.

Experimental Part

The examples below are carried out using standard techniques, which arewell known and routine to those of skill in the art, except whereotherwise described in detail. The examples are illustrative, but do notlimit the invention

The present investigation describes the isolation, purification,characterization, cloning and expression of the novel outer membraneprotein named protein E (pE) of H. influenzae and the novel truncatedrecombinant pE(A), which was discovered using a human IgD(λ) myelomaserum.

Materials and Methods Reagents

The type b H. influenzae strains MinnA and NTHi3655 were kindly obtainedfrom Robert S. Munson Jr. (Washington University School of Medicine (St.Louis, Mo.). The non-typable H. influenzae strain NTHi772 was a clinicalisolate from a nasopharyngeal swab culture at our Department (2). Aseries of different Haemophilus species was also analysed and isdescribed in Table 1. The human IgD myeloma whole serum IgD(λ) waspurchased from The Binding Site (Birmingham, England). To produce aspecific anti-pE antiserum, rabbits were immunized intramuscularly with200 μg of recombinant pE22-160 [pE(A)] emulsified in complete Freundsadjuvant (Difco, Becton Dickinson, Heidelberg, Germany) or pE41-68peptide conjugated to keyhole limpet hemocyanin (KLH) and boosted ondays 18 and 36 with the same dose of protein in incomplete Freundsadjuvans. Blood was drawn 2 to 3 weeks later. Resulting polyclonalantibodies were isolated by affinity chromatography using pE(A) or aspecific pE peptide (pE41-68) conjugated to CnBr-Sepharose (11).Horseradish peroxidase (HRP)-conjugated goat anti-human IgD was fromBiosource (Camarillo, Calif.). Rabbit anti-human IgD pAb were fromDakopatts (Gentofte, Denmark).

Fluoresceinisothiocyanate (FITC)-conjugated mouse anti-human IgD,HRP-conjugated rabbit anti-human light chains (κ and λ), andFITC-conjugated swine anti-rabbit polyclonal immunoglobulins werepurchased from Dakopatts.

Extraction and Purification of Protein E

H. influenzae type b (MinnA) was grown overnight in brain heart infusion(BHI) broth (Difco Laboratories, Detroit, Mich.) supplemented with NADand hemin (Sigma, St. Louis, Mo.), each at 10 μg/ml. After two washesthe bacteria were extracted in 0.05 M Tris-HCl-buffer (pH 8.8)containing 0.5% Empigen® (Calbiochem Novabiochem, Bedford, Mass.). Thebacterial suspension was mixed by magnetic stirring for 2 h at 37° C.After centrifugation at 8000×g for 20 min at 4° C., the supernatant wasfiltrated with sterile filter (0.45 μm; Sterivex-HV™, Millipore). H.influenzae extract in 0.5% Empigen® was applied to a Q-sepharose column(Amersham Pharmacia Biotech) equilibrated with 0.05 M Tris-HCl (pH 8.8)containing 6 M urea. The column was eluted using a 0 to 1 M NaCl lineargradient in the same buffer. Fractions that were detected by the IgD(λ)myeloma serum were pooled, dialyzed in Spectraphor membrane tubes(molecular weight cut off 6-8,000; Spectrum, Laguna hills, Calif.)against 0.05 M Tris-HCl, pH 8.8, and concentrated on YM100 discmembranes (molecular weight cut off 10,000; Amicon, Beverly, Mass.).

SDS-PAGE and Detection of Proteins on Membranes (Western Blot)

SDS-PAGE was run at 150 constant voltage using 10% Bis-Tris gels withrunning (MES), sample (LDS), and transfer buffer as well as a blottinginstrument from Novex (San Diego, Calif.). Samples were regularly heatedat 100° C. for 10 min. Gels were stained with Coomassie Brilliant BlueR-250 (13; Bio-Rad, Sundbyberg, Sweden). Electrophoretical transfer ofprotein bands from the gel to an immobilon-P membrane (Millipore,Bedford, Mass.) was carried out at 30 V for 2 to 3 h. After transfer,the immobilon-P membrane was blocked in PBS with 0.05% Tween 20(PBS-Tween) containing 5% milk powder. After several washings inPBS-Tween, the membrane was incubated with purified IgD myeloma protein(0.5 μg/ml, hu IgD(λ) myeloma; The Bindingsite) in PBS-Tween including2% milk powder for 1 h at room temperature. HRP-conjugated goatanti-human IgD diluted 1/1000 was added after several washings inPBS-Tween. After incubation for 40 min at room temperature and severaladditional washings in PBS-Tween, development was performed with ECLWestern blotting detection reagents (Amersham Pharmacia Biotech,Uppsala, Sweden).

Two-Dimensional SDS-Polyacrylamide Gel Electrophoresis (2-D PAGE) andWestern Blot

After ion exchange chromatography, Empigen® extracts of H. influenzae(MinnA) were subjected to isoelectric focusing (IEF) using the IPGphorIEF System (Amersham Pharmacia Biotech) (5,12). For gel calibration, astandard was used (cat. no. 161-0320; Bio-Rad). 2-D polyacrylamide gelswere electroblotted to Immobilon-PVDF filters (0.45 mm; Millipore,Bedford, US) at 120 mA over night. After saturation, incubation,blocking and washing steps were performed as described above.

Amino Acid Sequence Analysis

Automated amino acid sequence analysis was performed with an AppliedBiosystems (Foster City, Calif.) 470A gas-liquid solid phase sequenator.

Construction of a H. influenzae Genomic Library

Chromosomal DNA was prepared from strain 772 by using a modification ofthe method of Berns and Thomas (2,13). Briefly, an H. influenzae 772genomic library was constructed from 40 μg of DNA which was partiallydigested with Sau3A for 1 h. The cleaved DNA was fractionated on asucrose gradient (14). Fractions containing DNA fragments of appropriatesizes (2 to 7 kbp) were pooled, and the DNA was ligated toBamHI-digested pUC18 followed by transformation into Escherichia coliJM83 by electroporation using a Gene pulser (Bio-Rad, Richmond Calif.).The bacteria was plated onto LB agar supplemented with ampicillin andX-Gal (5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside).

Colony Immunoassay, DNA Isolation and Sequencing

The E. coli transformants, cultivated overnight on LB agar, weretransferred to nitrocellulose filters (Sartorius, Gottingen, Germany) bycovering the agar surfaces with dry filters. The plates were left for 15min, and the cells were lysed by exposure to saturated chloroform vaporfor 20 min. Residual protein-binding sites on the filters were blockedby incubating the filters in Tris balanced saline containing ovalbumin(50 mM Tris-hydrochloride, 154 mM NaCl, 1.5% ovalbumin [pH 7.4]) for 30min. After being blocked, the filters were incubated with human IgD(λ)for 30 min. HRP-conjugated anti-human IgD polyclonal antibodies wereadded after washes and the filters were incubated for 30 min. Allincubations were done at room temperature. Finally, filters weredeveloped using 4-chloro-1-naphtol and H₂O₂. Positive clones were pickedand pUC18 plasmid DNA containing NTHi772 genomic DNA was purified. Theresulting NTHi772 DNA insert was sequenced using the flanking primersM13+ and M13− and the Bigdye® Terminator Cycle Sequencing v. 2.0 Readyreaction sequencing kit (Perkin-Elmer, Foster City, Calif.). Theobtained insert sequence (3.55 kbp) corresponded to a stretch containingDNA encoding the proteins HI0175, HI0176, HI0177, and finally HI0178(15).

DNA Cloning and Protein Expression

All constructs were manufactured using PCR amplified fragments. pUC18containing NTHi 772 genomic DNA (HI0175 to HI0178) was used as template.Taq DNA polymerase was from Roche (Mannheim, Germany) and PCR conditionswere as recommended by the manufacturer. The open reading frames of thefour predictive proteins HI0175 to HI0178 were cloned, but only theprocedure describing cloning of HID (HI0178) has been included here.pE²²⁻¹⁶⁰ [designated pE(A)] was devoid of the endogenous signal peptideincluding amino acid residue glutamine²¹ and was amplified by PCR usingprimers 5′-ctcaggatccaaaggctgaacaaaatgatgtg-3′ (SEQ ID NO: 13) and5′-ggtgcagattaagcttttttttatcaactg-3′ (SEQ ID NO: 14) introducing therestriction enzyme sites BamHI and HindIII. To fuse 6 histidine residues(SEQ ID NO: 12) encoded by the expression vector, the pE²²⁻¹⁶⁰ stopcodon was mutated. The resulting 417 by open reading frame of the pegene was ligated into pET26(+) (Novagen, Darmstadt, Germany). To avoidpresumptive toxicity, the resulting plasmids were first transformed intothe host E. coli DH5α. Thereafter, the plasmids encoding pE and pE(A)were transformed into the expressing host BL21(DE3). In addition to fulllength pE and pE(A), a series of truncated pE variants weremanufactured. An outline is shown in FIG. 8. Primers containing BamHIand HindIII were used for all constructs. The procedures for thetruncated variants were as described above. All constructs weresequenced using the Bigdye® Terminator Cycle Sequencing v. 2.0 Readyreaction sequencing kit (Perkin-Elmer, Foster City, Calif.).

To produce recombinant proteins, bacteria were grown to mid-log phase(OD₆₀₀ 0.6 to 0.8) followed by induction with 1 mMisopropyl-1-thio-β-D-galactoside (IPTG) resulting in overexpression ofpE(A). When OD₆₀₀ reached 1.5 to 1.7, bacteria were harvested andinclusion bodies isolated according to a standard protocol. Recombinantproteins could be further purified by affinity chromatography usingnickel columns. Purified recombinant proteins were subsequently analysedby SDS-PAGE.

H. influenzae DNA Purification, PCR Conditions and Sequencing

Genomic DNA from H. influenzae clinical isolates was isolated using aDNeasy™ M Tissue kit (Qiagen, Hilden, Germany). Taq DNA polymerase wasfrom Roche (Mannheim, Germany) and PCR conditions were as recommended bythe manufacturer. To isolate the pe gene, the primer pair5′-gcatttattaggtcagtttattg-3′ (SEQ ID NO: 15) and5′-gaaggattatttctgatgcag-3′ (SEQ ID NO: 16), which anneal to theflanking genes HI0177 respectively HI0179, were used. Resulting PCRproducts (948 bp) were sequenced by gene-walking using the abovementioned primers in addition to the primers 5′-cttgggttacttaccgcttg-3′(SEQ ID NO: 17) and 5′-gtgttaaacttaacgtatg-3′ (SEQ ID NO: 18). Capillaryelectrophoresis was run on a Beckman CEQ 2000 using a dye-terminatorcycle sequencing kit (CEQ DTCS kit, Beckman Coulter, Stockholm, Sweden).Editing and alignment of the resulting DNA sequences were performedusing PHRED (CodonCode, Deadham, USA) and SEQUENCHER (MedProbe, Oslo,Norway).

Manufacture of a pE-Deficient H. influenzae (NTHi 3655 Δpe)

Genomic DNA isolated from NTHi 772 was used as template. The 5′- and3′-ends of pe including parts of the genes HI0177 and HI0179 wereamplified as two cassettes (815 bp and 836 bp, respectively) usingDyNAzyme™ II DNA polymerase (Finnzymes, Espoo, Finland) introducing therestriction enzyme sites XhoI and EcoRI respectively EcoRI and SpEI inaddition to specific uptake sequences in the two cassettes (18).Resulting PCR fragments were digested and cloned into pBluescript SK(+/−). A kanamycin resistance gene cassette (1282 bp) was obtained frompUC4K using the restriction enzyme site for EcoRI. After digestion, thePCR product was ligated into the truncated pe gene fragment containingparts of the HI0177 and HI0179 genes. H. influenzae strains Eagan andRM804 were transformed according to the M-IV method of Heriott et al.(19). Resulting mutants were verified by PCR and the pE expression wasanalysed by Western blot and flow cytometry.

Molecular Biology Softwares

Obtained sequences were compared with the available H. influenzae KW20genome (http://www.tigr.org) (15). The signal peptide was deduced usingthe SignalP V1.1 World Wide Web Prediction Server Center for BiologicalSequence Analysis (http://www.cbs.dtu.dk/services/SignalP/) (16). The pEhydrophobicity profile was analysed by the method of Kyte and Doolittle(17).

Animals, Surgical Procedures and Rat Otitis Media Model

Healthy male Sprague-Dawley rats, weighing 200-250 g were used. Allanimals were free of middle ear infections as determined byotomicroscopy before operation. At interventions, rats were anesthezisedwith methohexital (Brietal®, Elli Lilly and Company, Indianapolis, Ind.)intravenously or chloral hydrate (apoteksbolaget, Lund, Sweden)intraperitoneally. Bacteria for animal experiments were grown asdescribed above. After harvesting by centrifugation, the baceria wereresuspended in fresh culture media to a concentration of 2×10¹⁰ colonyforming units (cfu) for both NTHi 3655 and the corresponding pE mutant.Preparations were kept on ice until use. To induce acute otitis media(AOM), the middle ear was reached by a ventral midline incision in theneck, and approximately 0.05 ml of the bacterial suspension wasinstilled into the middle ear cavity. Otomicroscopy was performed ondays 3 and 5 post-operatively. Otitis media with purulent effusion,i.e., an opaque effusion and often pronounced dilatation of vessels onday 3, was referred to as AOM.

Results

Extraction and Separation of a H. influenzae Protein (pE) that isDetected by an IgD(λ) Myeloma Serum

It had previously been thought that non-typable H. influenzae (NTHi) donot bind IgD (19), whereas encapsulated H. influenzae strongly bind IgD.We discovered that an IgD(λ) myeloma serum specifically bound also toNTHi. A typical flow cytometry profile of the NTHi772 is shown inFIG. 1. A strong shift and increased fluorescence was found in thepresence of the IgD(λ) myeloma protein as compared to the controlwithout IgD.

To in detail analyse the H. influenzae outer membrane protein that wasdetected by the IgD(λ) myeloma, an outer membrane fraction wassolubilized in the detergent Empigen®. FIG. 1B demonstrates that a verystrong IgD-binding activity was obtained on Western blots for a proteinwith an apparent molecular weight of approximately 16 kDa. However, nodistinct protein band corresponding to the IgD-binding activity could bedetected on the Coomassie Brilliant blue-stained SDS-PAGE. Afterseparation on a Q-Sepharose column, the same outer membrane extract wasapplied to 2-dimensional gel electrophoresis and silver staining (FIG.1C). In parallel, a corresponding Western blot probed with human IgD(λ)was performed. The area where pE was localized could thus be encircled.However, no visible protein was observed (FIG. 1C).

Cloning of Protein E and Manufacture of a Non-Typable H. influenzaeMutant Devoid of pE

Since we could not detect any protein in the 2-D analysis afterseparation, an H. influenzae DNA library was constructed using thenon-typable H. influenzae (NTHi) strain 772. Genomic DNA containingfragments in the range of 2 to 7 kbp was ligated into pUC18 followed bytransformation into E. coli JM83. Transformants were analysed forIgD-binding using a colony immunoassay consisting of human IgD(λ) andHRP-conjugated anti-human IgD polyclonal antibodies. Three positivecolonies were found out of 20,000 colonies tested and were subjected toa second round of screening with IgD(λ). We sequenced one of thepositive clones and found a 3.55 kb insert containing DNA encoding forthe four proteins HI0175 to HI0178 according to the physical map of H.influenzae KW20 (15). To further verify the specific interaction withIgD(λ), the selected transformant was also analysed by flow cytometry.As can be seen in FIG. 2B, E. coli JM83 harbouring H. influenzae 772genomic DNA corresponding to the sequence encoding for HI0175 to HI0178was detected by IgD(λ) as compared to the negative control E. colitransformed with an empty vector only (FIG. 2A).

In addition to analysis of the E. coli JM83 clone, the four H.influenzae proteins (HI0175 to HI0178) were cloned into the expressionvector pET26(+) and produced in E. coli BL21DE3. The resultingrecombinant proteins were analysed by IgD(λ) on Western blots and HI0178was found to be the only protein that was detected by IgD(λ) (data notshown).

A non-typable H. influenzae (NTHi 3655) was mutated by introduction of akanamycin resistance gene cassette in the gene encoding for pE.Resulting mutants were confirmed by PCR and the absence of pE expressionwas proven by analysis of outer membrane proteins in Western blots usinga specific anti-pE antiserum (data not shown). The NTHi 3655Δpe mutantwas also tested by flow cytometry and a clearly decreased fluorescencewas found with the mutant as compared to the corresponding NTHi 3655wild type when analysed with a rabbit anti-pE monovalent antiserum and aFITC-conjugated goat anti-rabbit secondary pAb (FIGS. 2C and D).

Protein E was Detected in all H. influenzae, Whereas Other SubspeciesWere Negative

To analyse pE expression of clinical isolates and type strains of NTHi,we developed a direct binding flow cytometry assay consisting of theIgD(λ) serum and a FITC-conjugated secondary antibody directed againsthuman IgD. In initial experiments, bacteria collected at different timepoints were analysed for pE expression. No difference was observedregarding pE expression between logarithmic growing or stationary phasebacteria, suggesting that NTHi surface pE was not depending on thegrowth phase. Stationary phase bacteria were thus used in all furtheranalyses. Mean fluorescence intensity (mfi) per bacterial cell wasanalysed and a total of 22 NTHi strains were included in our study. Thefluorescence intensity varied between different NTHi strains, albeit pEwas detected in the majority of NTHi in this particular assay using theIgD(λ) myeloma serum as detection antibody (FIG. 3).

In other experiments specific rabbit anti-pE antibodies were used fordetection of surface exposed pE. The specific anti-pE antiserumspecifically recognized pE also in encapsulated strains of H.influenzae, H. aegypticus, and H. haemolyticus. (data not shown).

To further analyse pE expression levels, Empigen®-treated outer membraneextracts of various haemophilus species were tested in Western blotsusing IgD(λ) as detection antibody (Table 1). In these experiments, nodifferences between high and low expressing haemophilus strains werefound, i.e., in Western blots all strains displayed pE of the sameintensity and in the same position corresponding to 16 kDa. EncapsulatedH. influenzae (type a to f) also expressed pE as revealed by Westernblots (Table 1). For example, the pE expression in four H. influenzaecapsule type b (Hib) is compared to NTHi in FIG. 4. H. aegypticus, andH. haemolyticus expressed pE (Table 1), whereas for other relatedhaemophilus species, that were negative in flow cytometry (FIG. 3), nopE was detected in Western blot analyses. The specific anti-pE antiserumspecifically recognized pE also in encapsulated strains (data notshown).

TABLE 1 Western Blot (positive/ Encapsulated or non-typable (NT)negative; 0) 556 H. influenzae CCUG EF 6881 I Caps.type a pos 557 H.influenzae CCUG EF 7315 I Caps.type a pos 94 H. i. typ a pos 479 H.influenzae Minn A type b pos 547 H. influenzae Eagan type b pos 485 H.influenzae 85 05 30 b pos 539 H. influenzae D-22 Caps.type b pos 541 H.influenzae HK 695 Caps.type b pos 542 H. influenzae HK 691 Caps.type bpos 577 H. influenzae HK 713 Caps.type b pos 578 H. influenzae HK 714Caps.type b pos 582 H. influenzae HK 83458 caps type b pos 581 H.influenzae HK 163 caps type b pos 580 H. influenzae HK 729 caps type bpos 569 H. influenzae 17 B Dallas caps type b pos 568 H. influenzae DL42/2F4 caps type b pos 579 H. influenzae HK 720 caps type b pos 477 H.influenzae 6-460 caps type b pos 570 H. influenzae DL 42 caps type b posH. influenzae RM 804 no caps type b pos 583 H. influenzae HK 705 no capstype b pos 551 H. influenzae CCUG EF 4851 II Caps.type c pos 552 H.influenzae CCUG EF 4852 II Caps.type c pos 95 H. i. typ c pos 555 H.influenzae CCUG EF 6878 IV Caps.type d pos 560 H. influenzae CCUG EFNCTC 8470 Caps.type d pos 96 H. i. typ d pos 554 H. influenzae CCUG EF6877 IV Caps.type e pos 88 H. i. typ e A11/01 pos 89 H. i. typ e A76/01pos 90 H. i. typ e A77/99 pos 559 H. influenzae CCUG EF 15519 IICaps.type f pos 78 H. i. CCUG 15435 Caps.type f pos 91 H. i. typ f A1/01pos 92 H. i. typ f A58/01 pos 93 H. i. typ f A91/01 pos 67 H. i. NT6-9547 b.typ I pos 478 H. influenzae 6-601 NT pos 484 H. influenzae6-6200 NT NT pos 507 H. influenzae 6-102 NT NT pos 65 H. i. NT 7-68/99Claren. lavage pos 68 H. i. NT 7-758 pos 546 H. influenzae 6-9547 NT pos480 H. influenzae 772 NT pos 476 H. influenzae 6-115 NT pos 481 H.influenzae 6-504 NT pos 482 H. influenzae 6-7702 NT pos 483 H.influenzae 82 10 23 NT pos 486 H. influenzae 6-121 NT pos 506 H.influenzae 6-6267 NT pos 540 H. influenzae D-26 NT pos 543 H. influenzaeBuffalo 1479 NT pos 544 H. influenzae Buffalo C 7961 NT pos 64 H. i.56-2934 000428 NT pos 69 H. i. 7-120/99 bronch NT pos 70 H. i. 7-161/99bronch NT pos 66 H. i. S6-2952 000428 NT pos 105 H. i. RM 3655 NT pos531 H. aegypticus EF 628 NT, no b pos 73 H. aegypticus CCUG 25716 pos 74H. aegypticus CCUG 26840 pos 76 H. aegypticus CCUG 39154 pos 79 H.aegypticus HK 1247 pos 80 H. aegypticus HK 1229 pos 81 H. aegypticus HK1242 pos 82 H. i. biovar aegypticus HK 865 pos 83 H. i. biovaraegypticus HK 871 pos 84 H. i. biovar aegypticus HK 1222 pos 85 H. i.biovar aegypticus HK 1239 pos 86 BPF-like disease HK 1212 pos 87BPF-like disease HK 1213 pos 72 H. haemolyticus CCUG 15642 pos 101 H.haemolyticus 34669/83 pos 102 H. haemolyticus 47802/88 pos 103 H.haemolyticus 937016 pos 104 H. haemolyticus 74108/81 pos 520 H.parainfluenzae Biotype I HK 409 0 521 H. parainfluenzae Biotype II HK 230 58 59004 H. parainfl. biov. III 0 59 75834 H. parainfl. biov. III 0 6078909 H. parainfl. biov. III 0 97 H. parainfluenzae 947172 0 98 H.parainfluenzae 59257/91 0 99 H. parainfluenzae 59004/91 0 100 H.parainfluenzae 977101 0 545 H. parainfluenzae Buffalo 3198 NT 0 75 H.somnus CCUG 37617 0 512 H. parasuis 9918 0 516 H. parasuis 99 19 0 527H. parasuis EF 3712 0 524 H. paraphrophilus HK 319 0 525 H.paraphrophilus HK 415 0 517 H. paraphrophilus 12894 0 71 H. segnis CCUG14834 0 526 H. aphrophilus HK 327 0 529 H. aphrophilus 11832 A 0 532 H.pleurapneumoniae EF 9917 0 61 39612 Eikenella corrodens 0 62 49064Eikenella corrodens 0 63 959074 Eikenella corrodens 0 537 Actinobacillusactinomyc. HK 666 0 P. mult. 78908/90 0Recombinantly Produced pE22-160 [pE(A)] is Detected by IgD(λ)

In initial experiments, we tried to recombinantly manufacture pE, butonly minute concentrations were obtained. To maximize the protein yield,a truncated pE fragment consisting of amino acid residues lysine22 tolysine160 was constructed. The N-terminal signal peptide including theamino acid glutamine21 was thus removed and replaced with the leaderpeptide in addition to nine residues originating from the vectorpET26(+) (FIG. 5A). The truncated pE22-160 was designated pE(A) (FIG.5B). To confirm that the recombinant protein product corresponded to‘wild type’ pE, the recombinantly expressed pE(A) together with pEisolated from NTHi 772 was analysed by SDS-PAGE and Western blot usingthe IgD(λ) as a probe. As shown in FIG. 5D, the recombinant pE(A)significantly corresponded to wild type pE in SDS-PAGE. Furthermore,pE(A) produced in E. coli could be detected down to 0.01 microg by theIgD(λ) antiserum (FIG. 5E).

pE(A) was used for immunization of rabbits and after completion of theimmunization schedule as decribed in detail in Material and Methods, theanti-pE antiserum was purified on a column consisting of a calculatedimmuno-dominant peptide (amino acids pE41-68). The resulting an-tibodiesclearly detected pE both at the bacterial surface (FIG. 2C) and inWestern blots (not shown).

The DNA Sequence of the Protein E Gene and the Open Reading Frame

The DNA and amino acid sequence of pE1-160 from the strain NTHi 772 isoutlined in FIG. 6. The open reading frame (ORF) is 160 amino acids longand the predicted signal peptide has a length of 20 amino acids.Computer analysis suggested that the signal peptidase recognizes theamino acid residues alanine18 to lysine22 and cleaves between residuesisoleucine20 and glutamine21 (38). In parallel, the HID hydropathyprofile (39) shows that pE has a hydrophobic signal peptide, whereas therest of the molecule is mainly hydrophilic (FIG. 7).

To in detail determine the signal peptidase cleavage site, recombinantfull length pE was subjected to Edman degradation. However, theamino-terminal end of the pE polypeptide chain was probably blocked. Apossible explanation for this failure could be that the first amino acidwas a pyroglutamyl residue as previously described for the M.catarrhalis UspA family of proteins (11). However, attempts to removethis putative residue with pyroglutamate aminopeptidase failed. Incontrast to full length pE1-160, the N-terminal sequence for pE(A)(pE22-160) that lacks the endogenous H. influenzae signal peptide (FIG.5), was successfully characterized by Edman degradation and found tocontain the predicted vector sequence, i.e., the signal peptidase in E.coli cleaved at the correct position (FIG. 5A).

Protein E was sequenced in a series of different Haemophilus speciesincluding NTHi and encapsulated H. influenzae (Table 1). Interestingly,pE was extraordinary conserved. Only a few amino acids were pointmutated and these were mutated in most strains following a specificpattern (FIG. 6 and Table 2).

TABLE 2 Point mutations in the pe gene in different Haemophilus species when compared to H. influenzae Rd as reference strain^(a)). Number of  Pointstrains with Number mutation mutations (%) analysed  Ile20 > Thr2018  (58%) 31  Ala23 > Val23  5  (16%) 31  Glu24 > Lys24  1^(b))(3.2%) 31 Val28 > Met28  2 (6.5%) 31  Ala31 > Thr31 19  (61%) 31  Pro32 > Val32 3 (9.7%) 31  Pro32 > Ala32  5  (16%) 31  Ile41 > Val41  8  (26%) 31 Val47 > Ala47  3  (10%) 30  Arg76 > Lys76  2 (7.7%) 26 Ile107 > Val10716  (62%) 26 Lys153 > Glu153  1^(b))(3.2%) 13 Ala154 > Val154  2  (15%)13 Prolonged C-terminal (3 extra aa) SVDKK stop (=Rd)^(c)) 11  (85%) 13(SEQ ID NO: 19) SVDKKSAP stop  2  (15%) 13 (SEQ ID NO: 20) ^(a))The pegene was sequenced in encapsulated H. influenzae type a (n = 2), b (n =2), c (n = 2), d (n = 1), e (n = 2), and f (n = 3), NTHi (n = 8), H.influenzae biovar aegypticus (n = 6) and H. aegypticus (n = 5), usingflanking primers. ^(b))NTHi 772 (SEQ ID NO: 1) ^(c))Rd designates H.influenzae strain Rd.Different Fragments of pE can Easily be Produced in E. coli

Eight cDNA sequences derived from the full length pE were cloned intopET26b(+) and expressed in E. coli. Resulting proteins were purified onnickel resins with affinity for histidine tags (FIG. 8). The recombinantproteins covered the entire mature pE protein product and theirindividual lengths and positions were as demonstrated in FIG. 8A and thepurified products are outlined in FIG. 8B.

pE is a Crucial Virulence Factor in Rat Acute Otitis Media (AOM)

To investigate the role of pE as a virulence factor for NTHi, rats werechallenged in the middle ear with 10⁵ to 10⁹ NTHi 3655 Δpe or thecorresponding wild type NTHi 3655 (FIG. 9). Interestingly, a 100- to1,000-fold more of NTHi 3655 Δpe was required in order to induce asimilar AOM as compared to the wild type bacterium. Thus, pE is acrucial virulence factor for NTHi-induced AOM.

pE is Highly Immunogenic in a Defined Population

To measure antibody levels in children and blood donors, recombinantpE(A) was purified from E. coli (FIG. 5B) and used in an ELISA. Theresults of ELISA-analyses of antibodies against pE(A) are shown in FIG.9. Children less than 6 months of age had detectable IgG and IgA againstpE(A). IgG antibodies showed peak levels in children of 5 to 10 years ofage. In contrast, IgA antibodies increased gradually with increasing ageand the highest values were detected in the 70 to 80-year age group.

Useful Epitopes

The B-cell epitopes of a protein are mainly localized at its surface. Topredict B-cell epitopes of protein E polypeptides two methods werecombined: 2D-structure prediction and antigenic index prediction. The2D-structure prediction was made using the PSIPRED program (from DavidJones, Brunel Bioinformatics Group, Dept. Biological Sciences, BrunelUniversity, Uxbridge UB8 3PH, UK). The antigenic index was calculated onthe basis of the method described by Jameson and Wolf (CABIOS 4:181-186[1988]). The parameters used in this program are the antigenic index andthe minimal length for an antigenic peptide. An antigenic index of 0.9for a minimum of 5 consecutive amino acids was used as threshold in theprogram. Peptides comprising good, potential B-cell epitopes are listedin table 3. These can be useful (preferably conjugated or recombinantlyjoined to a larger protein) in a vaccine composition for the preventionof ntHi infections, as could similar peptides comprising conservativemutations (preferably 70, 80, 85, 95, 99 or 100% identical to thesequences of table 3) or truncates comprising 5 or more (e.g. 6, 7, 8,9, 10, 11, 12, 15, 20 or 25) amino acids therefrom or extensionscomprising e. g. 1, 2, 3, 5, 10 further amino acids at N- and/orC-terminal ends of the peptide from the native context of protein E (SEQID NO: 1 or natural homologues thereof as shown in Table 2 above)polypeptide which preserve an effective epitope which can elicit animmune response in a host against the protein E polypeptide.

TABLE 3 Potential B-cell epitopes from SEQ ID NO: 1(or natural homologues thereof) Position Sequence  21QKAKQND (SEQ ID NO: 21)  21 QKVKQND (SEQ ID NO: 22)  21QKAQQND (SEQ ID NO: 23)  21 QKVQQND (SEQ ID NO: 24)  59DNQEPQ (SEQ ID NO: 25)  82 PEPKRYARSVRQ (SEQ ID NO: 26) 106QIRTDFYDEFWGQG (SEQ ID NO: 27) 106 QVRTDFYDEFWGQG (SEQ ID NO: 28) 123APKKQKKH (SEQ ID NO: 29) 136 PDTTL (SEQ ID NO: 30)

Conclusions

The surface exposed Haemophilus outer membrane protein pE is a crucialvirulence factor for NTHi-induced AOM, is highly immunogenic in adefined population and thus is a very suitable vaccine candidate for avariety of human diseases.

REFERENCES

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2. Janson, H., L.-O. Hedén, A. Grubb, M. Ruan, and A. Forsgren. 1991.Protein D, an immunoglobulin D-binding protein of Haemophiliusinfluenzae: cloning, nucleotide sequence, and expression in Escherichiacoli. Infect. Immun. 59:119.

3. Janson, H., Å. Melhus, A. Hermansson, and A. Forsgren. 1994. ProteinD, the glycerophosphodiester phosphodiesterase from Haemophilusinfluenzae with affinity for human immunoglobulin D, influencesvirulence in a rat otitis model. Infect. Immun. 62:4848.

4. Janson, H., B. Carlén, A. Cervin, A. Forsgren, A. Björk-Magnusdottir,S. Lindberg, and T. Runer. 1999. Effects on the ciliated epithelium ofprotein D-producing and -nonproducing nontypeable Haemophilus influenzaein nasopharyngeal tissue cultures. J. Infect. Dis. 180:737.

5. Ahren, I. L., H. Janson, A. Forsgren, K. Riesbeck. 2001. Protein Dexpression promotes the adherence and internalization of non-typeableHaemophilus influenzae into human monocytic cells. Microb. Pathog.31:151.

6. Forsgren, A. and Grubb, A. (1979) Many bacterial species bind humanIgD. J. Immunol. 122, 1468-1472.

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1-80. (canceled)
 81. A method for the prophylaxis or treatment of aninfection in an individual, comprising administering to an individual inneed thereof a pharmaceutically effective amount of a vaccinecomposition selected from the group consisting of (i) a vaccinecomposition comprising a protein having an amino acid sequence asdescribed in SEQ ID NO: 1, or a fragment thereof, wherein the fragmentcomprises an amino acid sequence having at least 15 contiguous aminoacids from the amino acid sequence of SEQ ID NO: 1 and is capable ofraising an immune response, if necessary when coupled to a carrier, thatrecognizes the polypeptide of SEQ ID NO: 1; (ii) a vaccine compositioncomprising a recombinant polypeptide, or a fragment thereof, wherein thepolypeptide comprises the sequence of SEQ ID NO: 1, wherein the aminoacids in position 1 to 21 of SEQ ID NO: 1 have been deleted or replacedby one or more amino acids, and wherein the fragment comprises an aminoacid sequence having at least 15 contiguous amino acids from the aminoacid sequence of the polypeptide and is capable of raising an immuneresponse, if necessary when coupled to a carrier, that recognizes thepolypeptide; (iii) a vaccine composition comprising a nucleic acidsequence encoding the protein or fragment of claim 1; and (iv) a vaccinecomposition comprising a polypeptide, or a fragment thereof, wherein thepolypeptide comprises an amino acid sequence that varies from SEQ ID NO:1 at one or more positions, wherein the variation(s) are selected fromthe group consisting of a deletion of a signal peptide (amino acids1-20) of SEQ ID NO: 1, a Thr substitution of lie at position 20 of SEQID NO: 1, a Val substitution of Ala at position 23 of SEQ ID NO: 1, aGin substitution of Lys at position 24 of SEQ ID NO: 1, a Metsubstitution of Val at position 28 of SEQ ID NO: 1, a Thr substitutionof Ala at position 31 of SEQ ID NO: 1, a Val substitution of Ile atposition 41 of SEQ ID NO: 1, an Ala substitution of Val at position 47of SEQ ID NO: 1, a Lys substitution of Arg at position 76 of SEQ ID NO:1, a Val substitution of lie at position 107 of SEQ ID NO: 1, a Lyssubstitution of Gly at position 152 of SEQ ID NO: 1, a Val substitutionof Ala at position 154 of SEQ ID NO: 1, a Ser-Ala-Pro addition at theC-terminus of SEQ ID NO: 1, a Val substitution of Pro at position 32 ofSEQ ID NO: 1, and an Ala substitution of Pro at position 32 of SEQ IDNO: 1, wherein the fragment comprises an amino acid sequence having atleast 15 contiguous amino acids from the amino acid sequence of thepolypeptide.
 82. The method of claim 81, wherein the infection is causedby Haemophilus influenzae.
 83. The method of claim 82, wherein theHaemophilus influenza is encapsulated or non-typable.
 84. The method ofclaim 83, wherein the infection is otitis media, sinusitis or a lowerrespiratory tract infection.